# Tagged with #ploidy 2 documentation articles | 2 announcements | 29 forum discussions

Created 2013-08-23 21:34:04 | Updated 2014-10-24 16:21:11 | Tags: unifiedgenotyper haplotypecaller ploidy

Use HaplotypeCaller!

The HaplotypeCaller is a more recent and sophisticated tool than the UnifiedGenotyper. Its ability to call SNPs is equivalent to that of the UnifiedGenotyper, its ability to call indels is far superior, and it is now capable of calling non-diploid samples. It also comprises several unique functionalities such as the reference confidence model (which enables efficient and incremental variant discovery on ridiculously large cohorts) and special settings for RNAseq data.

As of GATK version 3.3, we recommend using HaplotypeCaller in all cases, with no exceptions.

Caveats for older versions

If you are limited to older versions for project continuity, you may opt to use UnifiedGenotyper in the following cases:

• If you are working with non-diploid organisms (UG can handle different levels of ploidy while older versions of HC cannot)
• If you are working with pooled samples (also due to the HC’s limitation regarding ploidy)
• If you want to analyze more than 100 samples at a time (for performance reasons) (versions 2.x)

Created 2012-07-26 14:50:55 | Updated 2014-10-24 00:55:34 | Tags: unifiedgenotyper ploidy haploid intermediate

In general most GATK tools don't care about ploidy. The major exception is, of course, at the variant calling step: the variant callers need to know what ploidy is assumed for a given sample in order to perform the appropriate calculations.

### Ploidy-related functionalities

As of version 3.3, the HaplotypeCaller and GenotypeGVCFs are able to deal with non-diploid organisms (whether haploid or exotically polyploid). In the case of HaplotypeCaller, you need to specify the ploidy of your non-diploid sample with the -ploidy argument. HC can only deal with one ploidy at a time, so if you want to process different chromosomes with different ploidies (e.g. to call X and Y in males) you need to run them separately. On the bright side, you can combine the resulting files afterward. In particular, if you’re running the -ERC GVCF workflow, you’ll find that both CombineGVCFs and GenotypeGVCFs are able to handle mixed ploidies (between locations and between samples). Both tools are able to correctly work out the ploidy of any given sample at a given site based on the composition of the GT field, so they don’t require you to specify the -ploidy argument.

For earlier versions (all the way to 2.0) the fallback option is UnifiedGenotyper, which also accepts the -ploidy argument.

### Cases where ploidy needs to be specified

1. Native variant calling in haploid or polyploid organisms.
2. Pooled calling where many pooled organisms share a single barcode and hence are treated as a single "sample".
3. Pooled validation/genotyping at known sites.

For normal organism ploidy, you just set the -ploidy argument to the desired number of chromosomes per organism. In the case of pooled sequencing experiments, this argument should be set to the number of chromosomes per barcoded sample, i.e. (Ploidy per individual) * (Individuals in pool).

## Important limitations

Several variant annotations are not appropriate for use with non-diploid cases. In particular, InbreedingCoeff will not be annotated on non-diploid calls. Annotations that do work and are supported in non-diploid use cases are the following: QUAL, QD, SB, FS, AC, AF, and Genotype annotations such as PL, AD, GT, etc.

You should also be aware of the fundamental accuracy limitations of high ploidy calling. Calling low-frequency variants in a pool or in an organism with high ploidy is hard because these rare variants become almost indistinguishable from sequencing errors.

Created 2014-10-23 18:53:52 | Updated 2015-05-12 17:24:14 | Tags: Troll haplotypecaller ploidy release-notes genotype-refinement genotypegvcfs gatk3

GATK 3.3 was released on October 23, 2014. Itemized changes are listed below. For more details, see the user-friendly version highlights.

## Haplotype Caller

• Improved the accuracy of dangling head merging in the HC assembler (now enabled by default).
• Physical phasing information is output by default in new sample-level PID and PGT tags.
• Added the --sample_name argument. This is a shortcut for people who have multi-sample BAMs but would like to use -ERC GVCF mode with a particular one of those samples.
• Support added for generalized ploidy. The global ploidy is specified with the -ploidy argument.
• Fixed IndexOutOfBounds error associated with tail merging.

## Variant Recalibrator

• New --ignore_all_filters option. If specified, the variant recalibrator will ignore all input filters and treat sites as unfiltered.

## GenotypeGVCFs

• Support added for generalized ploidy. The global ploidy is specified with the -ploidy argument.
• Bug fix for the case when we assumed ADs were in the same order if the number of alleles matched.
• Changed the default GVCF GQ Bands from 5,20,60 to be 1..60 by 1s, 60...90 by 10s and 99 in order to give finer resolution.
• Bug fix in the exact model when calling multi-allelic variants. QUAL field is now more accurate.

## RNAseq analysis

• Bug fixes for working with unmapped reads.

## CalculateGenotypePosteriors

• New annotation for low- and high-confidence possible de novos (only annotates biallelics).
• FamilyLikelihoodsUtils now add joint likelihood and joint posterior annotations.
• Restricted population priors based on discovered allele count to be valid for 10 or more samples.

## DepthOfCoverage

• Fixed rare bug triggered by hash collision between sample names.

## SelectVariants

• Updated the --keepOriginalAC functionality in SelectVariants to work for sites that lose alleles in the selection.

• Read groups that are excluded by sample_name, platform, or read_group arguments no longer appear in the header.
• The performance penalty associated with filtering by read group has been essentially eliminated.

## Annotations

• StrandOddsRatio is now a standard annotation that is output by default.
• We used to output zero for FS if there was no data available at a site, now we omit FS.
• Extensive rewrite of the annotation documentation.

## Queue

• Fixed issue related to spaces in job names that were fine in GridEngine 6 but break in (Son of) GE8.
• Improved scatter contigs algorithm to be fairer when splitting many contigs into few parts (contributed by @smowton)

## Documentation

• We now generate PHP files instead of HTML.
• We now output a JSON version of the tool documentation that can be used to generate wrappers for GATK commands.

## Miscellaneous

• Output arguments --no_cmdline_in_header, --sites_only, and --bcf for VCF files, and --bam_compression, --simplifyBAM, --disable_bam_indexing, and --generate_md5 for BAM files moved to the engine level.
• htsjdk updated to version 1.120.1620

Created 2014-08-27 18:39:39 | Updated 2014-12-16 03:19:38 | Tags: haplotypecaller ploidy haploid polyploid

Until now, HaplotypeCaller was only capable of calling variants in diploid organisms due to some assumptions made in the underlying algorithms. I'm happy to announce that we now have a generalized version that is capable of handling any ploidy you specify at the command line!

This new feature, which we're calling "omniploidy", is technically still under development, but we think it's mature enough for the more adventurous to try out as a beta test ahead of the next official release. We'd especially love to get some feedback from people who work with non-diploids on a regular basis, so we're hoping that some of you microbiologists and assorted plant scientists will take it out for a spin and let us know how it behaves in your hands.

It's available in the latest nightly builds; just use the -ploidy argument to give it a whirl. If you have any questions or feedback, please post a comment on this article in the forum.

Caveat: the downstream tools involved in the new GVCF-based workflow (GenotypeGVCFs and CombineGVCFs) are not yet capable of handling non-diploid calls correctly -- but we're working on it.

#### UPDATE:

We have added omniploidy support to the GVCF handling tools, with the following limitations:

• When running, you need to indicate the sample ploidy that was used to generate the GVCFs with -ploidy. As usual 2 is the default ploidy.

• The system does not support mixed ploidy across samples nor positions. An error message will be thrown if you attempt to genotype GVCFs that have a mixture, or that have some genotype whose ploidy does not match the -ploidy argument.

#### LATEST UPDATE:

As of GATK version 3.3-0, the GVCF tools are capable of ad-hoc ploidy detection, and can handle mixed ploidies. See the release highlights for details.

Created 2016-04-27 16:23:36 | Updated | Tags: ploidy genotypegvcfs combinegvcfs sex-chromosomes sample-ploidy

Hi,

I am setting up a pipeline for HaplotypeCaller and there is something I do not understand. In the manual pages of CombineGVCFs and GenotypeGVCFs it is said: "This tool is able to handle any ploidy (or mix of ploidies) intelligently; there is no need to specify ploidy for non-diploid organisms".

But then there is the description of the "--sample_ploidy" argument. Do I have to set the number of samples?

And if I want to genotype the X chromosome for a set of samples (for which, depending on the sex, HC was run with ploidy 1 or ploidy 2), do I have to do something special?

Many thanks, Federico

Created 2016-02-03 20:16:19 | Updated | Tags: haplotypecaller ploidy

I have NGS data from an organism that is sometimes found to be aneuploid (but usually diploid.) I am trying to determine the ploidy of the individual I have sequenced from my population of interest. I have ~100X coverage, but the best reference is so distantly-related that the normal SNP coverage plots that are used to estimate ploidy are too messy to interpret. I was hoping that I could use HaplotypeCaller here to help determine the number of haplotypes per chromosome (where 2 haplotypes/alleles per position indicates diploidy). I can't figure out how to interpret the resulting VCF file well enough to address this question.

If HaplotypeCaller will not be sufficient, are there any other frequently used options to determine ploidy (or number of alleles/haplotypes per position)?

Thanks for any assistance.

Alex

Created 2015-12-02 23:31:39 | Updated | Tags: unifiedgenotyper ploidy gatk variant-calling

I am using the Gatk v3.1 UnifiedGenotyper for variant calling of some GBS type data in the plant genus Boechera. I have diploids as well as triploids, where I have the ploidy from a prior microsat run. The diploids work out well (I get some 150k variable loci), but I can't seem to get variants for the triploids.

Here's my initial call for the triploids:

Program Args: -T UnifiedGenotyper -R /home/A01768064/assembly/Bstricta_278_v1.fa -I mytripbam.list -o boechera_triploids.vcf -nt 22 -glm SNP -hets 0.001 -mbq 20 -ploidy 3 -pnrm EXACT_GENERAL_PLOIDY -stand_call_conf 50 -maxAltAlleles 2

I was able to call the triploids with the diploid option, but - obviously - this is not what I want. I additionally ran the following relaxed stringency options.

hets 0.01 mbq 10 hets 0.1 mbq 10

None of them return any variants.

The read group for one example file:

@RG ID:CR1308 LB:CR1308 SM:CR1308 PL:ILLUMINA (with unique values for each sample; note that in the output vcf, the samples are appearing in the header line)

Additionally, I attached the slurm log file for the last mentioned run.

I am at a complete loss, what am I missing here?

Created 2015-08-31 11:58:59 | Updated | Tags: baserecalibrator best-practices ploidy pooling

Dear GATK Team,

baserecalibrator is in the newest Best Practices recommendations. Does this tool support or would you recommend it's usage for samples with ploidy higher then 2 (e.g. pooled samples)?

Thanks! Bernt

Created 2015-08-30 22:27:03 | Updated 2015-08-30 22:30:48 | Tags: haplotypecaller ploidy pooled-calls

Hello everyone,

I was reading the haplotype caller documentation and noticed the "--sample_ploidy/-ploidy" flag. The description reads "Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy)."

My question is, what exactly is a pooled experiment? Is it when I have multiple samples? I have separate files for each of my 8 samples and the organism only has one chromosome. So would the number I set be 8*1? Or is this pooled number for multiple samples within a file, and in which case, I would specify 1 instead of 8.

Thanks! Raymosrunerx

Created 2015-08-26 01:25:39 | Updated | Tags: haplotypecaller ploidy runtime-error

Greetings! I am running HaplotypeCaller on a haploid data set. It works perfectly leaving the default ploidy at 2, but I get the following error when I set it to 1:

INFO 21:05:57,644 HelpFormatter - -------------------------------------------------------------------------------- INFO 21:05:57,648 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.2-2-gec30cee, Compiled 2014/07/17 15:22:03 INFO 21:05:57,648 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 21:05:57,651 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 21:05:57,658 HelpFormatter - Program Args: -T HaplotypeCaller -R Ref.fa -I aln-pe_RG_sorted_dedup_realigned.bam -o aln-pe_RG_sorted_dedup_realigned_HC_ploidy1.vcf -ploidy 1 -maxAltAlleles 2 INFO 21:05:57,666 HelpFormatter - Executing as mzilvers@f2c06 on Linux 2.6.32-504.8.1.el6.x86_64 amd64; OpenJDK 64-Bit Server VM 1.7.0_75-mockbuild_2015_01_20_23_39-b00. INFO 21:05:57,667 HelpFormatter - Date/Time: 2015/08/25 21:05:57 INFO 21:05:57,667 HelpFormatter - -------------------------------------------------------------------------------- INFO 21:05:57,668 HelpFormatter - -------------------------------------------------------------------------------- INFO 21:05:57,913 GenomeAnalysisEngine - Strictness is SILENT INFO 21:05:58,027 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 INFO 21:05:58,040 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 21:05:58,067 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.03 INFO 21:05:58,079 HCMappingQualityFilter - Filtering out reads with MAPQ < 20 INFO 21:05:58,213 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 21:05:58,302 GenomeAnalysisEngine - Done preparing for traversal INFO 21:05:58,303 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 21:05:58,305 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 21:05:58,306 ProgressMeter - Location | active regions | elapsed | active regions | completed | runtime | runtime INFO 21:05:58,520 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units INFO 21:05:58,828 AFCalcFactory - Requested ploidy 1 maxAltAlleles 2 not supported by requested model EXACT_INDEPENDENT looking for an option INFO 21:05:58,829 AFCalcFactory - Selecting model EXACT_GENERAL_PLOIDY INFO 21:06:28,312 ProgressMeter - Starting 0.0 30.0 s 49.6 w 100.0% 30.0 s 0.0 s

##### ERROR stack trace

java.lang.NullPointerException at org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.GeneralPloidyExactAFCalc.assignGenotype(GeneralPloidyExactAFCalc.java:559) at org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.GeneralPloidyExactAFCalc.subsetAlleles(GeneralPloidyExactAFCalc.java:527) at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:286) at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:335) at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:320) at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:310) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.isActive(HaplotypeCaller.java:844) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.addIsActiveResult(TraverseActiveRegions.java:618) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.access$800(TraverseActiveRegions.java:78) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$ActiveRegionIterator.hasNext(TraverseActiveRegions.java:378) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:268) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:273) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78) at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314) at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107)

##### ERROR A GATK RUNTIME ERROR has occurred (version 3.2-2-gec30cee):

Any help is appreciated!

Created 2015-07-17 22:01:12 | Updated 2015-07-17 22:14:12 | Tags: haplotypecaller ploidy haploid genotypegvcfs combinegvcfs

Hi,

I'm attempting to run GenotypeGVCFs on a cohort of ~4200 human male samples with targeted sequencing. I'm following the current DNA-Seq guidelines for cohort genotyping, with GATK v3.4-0. For each sample, I ran HaplotypeCaller separately for diploid and haploid (i.e., chrX non-PAR) regions, specifying --ploidy 1 for the haploid regions, then combined the resulting two GVCFs with CombineGVCFs. I then combined the per-sample GVCFs into groups of 64 samples using CombineGVCFs. Finally, I ran GenotypeGVCFs with all samples separately for groups of ~100 small target intervals (baits). Every group of target intervals ran fine without error in about 4 hours with ~5GB of RAM, except for the non-PAR chrX regions, which were haploid for all samples.

For the haploid regions, GATK hangs on the very first base, slowly increasing memory usage, then eventually runs out of memory and exits. The estimated runtime keeps increasing without making any progress. The last run exited after 12 hours without making any progress. This happens no matter how much memory I specify (up to 128 GB).

Interestingly, a PAR region of chromosome X run with --ploidy 2 in HaplotypeCaller worked with no problem.

The inputted GVCF files to GenotypeGVCFs are uncompressed and were indexed by CombineGVCFs.

I'm using default settings for GenotypeGVCFs, except for the following:

 --standard_min_confidence_threshold_for_calling 20 --standard_min_confidence_threshold_for_emitting 10 --dbsnp dbSNP142.20150416.GRCh37.for-GATK.chr1-MT.vcf.gz 

I tried running GenotypeGVCFs with the latest v3.4-46 release, but the same problem occurred.

Below is example output:

INFO 10:57:51,803 HelpFormatter - --------------------------------------------------------------------------------- INFO 10:57:51,810 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.4-46-gbc02625, Compiled 2015/07/09 17:38:12 INFO 10:57:51,811 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 10:57:51,811 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 10:57:51,818 HelpFormatter - Program Args: -T GenotypeGVCFs -R /tmp/12715944.hpc-pbs.hpcc.usc.edu/hs37m.fa --dbsnp dbSNP142.20150416.GRCh37.for-GATK.chr1-MT.vcf.gz --standard_min_confidence_threshold_for_calling 20 --standard_min_confidence_threshold_for_emitting 10 [LONG LIST OF VARIANT FILES OMITTED] --out gatk.hc.combined.genotyped.chunk117.vcf.gz -L split_117.intervals --log_to_file gatk.hc.combined.genotyped.chunk117.log INFO 10:57:51,824 HelpFormatter - Executing as cedlund@hpc1130.m10g.hpcc.usc.edu on Linux 2.6.32-504.12.2.el6.x86_64 amd64; Java HotSpot(TM) 64-Bit Server VM 1.7.0_51-b13. INFO 10:57:51,825 HelpFormatter - Date/Time: 2015/07/17 10:57:51 INFO 10:57:51,826 HelpFormatter - --------------------------------------------------------------------------------- INFO 10:57:51,826 HelpFormatter - --------------------------------------------------------------------------------- INFO 10:57:56,331 GenomeAnalysisEngine - Strictness is SILENT INFO 10:57:56,671 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 INFO 10:59:03,550 IntervalUtils - Processing 154370 bp from intervals WARN 10:59:03,615 IndexDictionaryUtils - Track dbsnp doesn't have a sequence dictionary built in, skipping dictionary validation INFO 10:59:03,766 GenomeAnalysisEngine - Preparing for traversal INFO 10:59:03,768 GenomeAnalysisEngine - Done preparing for traversal INFO 10:59:03,768 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 10:59:03,769 ProgressMeter - | processed | time | per 1M | | total | remaining INFO 10:59:03,770 ProgressMeter - Location | sites | elapsed | sites | completed | runtime | runtime INFO 10:59:04,283 GenotypeGVCFs - Notice that the -ploidy parameter is ignored in GenotypeGVCFs tool as this is automatically determined by the input variant files INFO 10:59:57,328 ProgressMeter - X:51033766 216.0 53.0 s 68.9 h 0.2% 7.2 h 7.2 h INFO 11:00:27,330 ProgressMeter - X:51035366 216.0 83.0 s 4.5 d 1.2% 111.5 m 110.1 m INFO 11:00:57,353 ProgressMeter - X:51035366 216.0 113.0 s 6.1 d 1.2% 2.5 h 2.5 h INFO 11:01:27,354 ProgressMeter - X:51035366 216.0 2.4 m 7.7 d 1.2% 3.2 h 3.2 h INFO 11:01:57,356 ProgressMeter - X:51035366 216.0 2.9 m 9.3 d 1.2% 3.9 h 3.8 h INFO 11:02:27,358 ProgressMeter - X:51035366 216.0 3.4 m 10.9 d 1.2% 4.5 h 4.5 h INFO 11:02:57,882 ProgressMeter - X:51035366 216.0 3.9 m 12.5 d 1.2% 5.2 h 5.2 h INFO 11:03:27,884 ProgressMeter - X:51035366 216.0 4.4 m 14.2 d 1.2% 5.9 h 5.8 h INFO 11:03:57,885 ProgressMeter - X:51035366 216.0 4.9 m 15.8 d 1.2% 6.6 h 6.5 h INFO 11:04:27,887 ProgressMeter - X:51035366 216.0 5.4 m 17.4 d 1.2% 7.3 h 7.2 h INFO 11:04:58,976 ProgressMeter - X:51035366 216.0 5.9 m 19.0 d 1.2% 7.9 h 7.8 h INFO 11:05:28,977 ProgressMeter - X:51035366 216.0 6.4 m 2.9 w 1.2% 8.6 h 8.5 h INFO 11:05:58,979 ProgressMeter - X:51035366 216.0 6.9 m 3.2 w 1.2% 9.3 h 9.2 h INFO 11:06:28,981 ProgressMeter - X:51035366 216.0 7.4 m 3.4 w 1.2% 10.0 h 9.8 h INFO 11:06:58,982 ProgressMeter - X:51035366 216.0 7.9 m 3.6 w 1.2% 10.6 h 10.5 h INFO 11:07:28,984 ProgressMeter - X:51035366 216.0 8.4 m 3.9 w 1.2% 11.3 h 11.2 h INFO 11:07:58,986 ProgressMeter - X:51035366 216.0 8.9 m 4.1 w 1.2% 12.0 h 11.8 h INFO 11:08:30,497 ProgressMeter - X:51035366 216.0 9.4 m 4.3 w 1.2% 12.7 h 12.5 h INFO 11:09:30,568 ProgressMeter - X:51035366 216.0 10.4 m 4.8 w 1.2% 14.0 h 13.8 h INFO 11:10:32,779 ProgressMeter - X:51035366 216.0 11.5 m 5.3 w 1.2% 15.4 h 15.2 h INFO 11:11:33,479 ProgressMeter - X:51035366 216.0 12.5 m 5.7 w 1.2% 16.8 h 16.6 h INFO 11:12:35,360 ProgressMeter - X:51035366 216.0 13.5 m 6.2 w 1.2% 18.2 h 17.9 h INFO 11:13:35,445 ProgressMeter - X:51035366 216.0 14.5 m 6.7 w 1.2% 19.5 h 19.3 h INFO 11:14:39,689 ProgressMeter - X:51035366 216.0 15.6 m 7.2 w 1.2% 20.9 h 20.7 h INFO 11:15:40,505 ProgressMeter - X:51035366 216.0 16.6 m 7.6 w 1.2% 22.3 h 22.0 h INFO 11:16:41,140 ProgressMeter - X:51035366 216.0 17.6 m 8.1 w 1.2% 23.7 h 23.4 h INFO 11:17:41,956 ProgressMeter - X:51035366 216.0 18.6 m 8.6 w 1.2% 25.0 h 24.7 h INFO 11:18:41,958 ProgressMeter - X:51035366 216.0 19.6 m 9.0 w 1.2% 26.4 h 26.0 h INFO 11:19:44,493 ProgressMeter - X:51035366 216.0 20.7 m 9.5 w 1.2% 27.8 h 27.4 h INFO 11:20:49,749 ProgressMeter - X:51035366 216.0 21.8 m 10.0 w 1.2% 29.2 h 28.8 h INFO 11:21:53,414 ProgressMeter - X:51035366 216.0 22.8 m 10.5 w 1.2% 30.6 h 30.3 h INFO 11:22:58,174 ProgressMeter - X:51035366 216.0 23.9 m 11.0 w 1.2% 32.1 h 31.7 h INFO 11:24:01,211 ProgressMeter - X:51035366 216.0 25.0 m 11.5 w 1.2% 33.5 h 33.1 h INFO 11:25:05,051 ProgressMeter - X:51035366 216.0 26.0 m 12.0 w 1.2% 34.9 h 34.5 h INFO 11:26:07,782 ProgressMeter - X:51035366 216.0 27.1 m 12.4 w 1.2% 36.3 h 35.9 h INFO 11:27:10,933 ProgressMeter - X:51035366 216.0 28.1 m 12.9 w 1.2% 37.8 h 37.3 h INFO 11:28:20,854 ProgressMeter - X:51035366 216.0 29.3 m 13.5 w 1.2% 39.3 h 38.8 h INFO 11:29:28,165 ProgressMeter - X:51035366 216.0 30.4 m 14.0 w 1.2% 40.8 h 40.3 h INFO 11:30:28,575 ProgressMeter - X:51035366 216.0 31.4 m 14.4 w 1.2% 42.2 h 41.6 h INFO 11:31:36,673 ProgressMeter - X:51035366 216.0 32.5 m 14.9 w 1.2% 43.7 h 43.1 h INFO 11:32:45,497 ProgressMeter - X:51035366 216.0 33.7 m 15.5 w 1.2% 45.2 h 44.7 h INFO 11:33:49,205 ProgressMeter - X:51035366 216.0 34.8 m 16.0 w 1.2% 46.7 h 46.1 h INFO 11:34:49,226 ProgressMeter - X:51035366 216.0 35.8 m 16.4 w 1.2% 48.0 h 47.4 h INFO 11:35:54,571 ProgressMeter - X:51035366 216.0 36.8 m 16.9 w 1.2% 49.5 h 48.8 h INFO 11:36:59,402 ProgressMeter - X:51035366 216.0 37.9 m 17.4 w 1.2% 50.9 h 50.3 h INFO 11:38:03,427 ProgressMeter - X:51035366 216.0 39.0 m 17.9 w 1.2% 52.3 h 51.7 h INFO 11:39:12,036 ProgressMeter - X:51035366 216.0 40.1 m 18.4 w 1.2% 53.9 h 53.2 h INFO 11:40:15,472 ProgressMeter - X:51035366 216.0 41.2 m 18.9 w 1.2% 55.3 h 54.6 h INFO 11:41:22,184 ProgressMeter - X:51035366 216.0 42.3 m 19.4 w 1.2% 56.8 h 56.1 h INFO 11:42:24,992 ProgressMeter - X:51035366 216.0 43.4 m 19.9 w 1.2% 58.2 h 57.5 h INFO 11:43:30,745 ProgressMeter - X:51035366 216.0 44.4 m 20.4 w 1.2% 59.7 h 58.9 h INFO 11:44:41,392 ProgressMeter - X:51035366 216.0 45.6 m 21.0 w 1.2% 61.3 h 60.5 h INFO 11:45:51,136 ProgressMeter - X:51035366 216.0 46.8 m 21.5 w 1.2% 62.8 h 62.0 h INFO 11:46:59,056 ProgressMeter - X:51035366 216.0 47.9 m 22.0 w 1.2% 64.3 h 63.5 h INFO 11:48:09,266 ProgressMeter - X:51035366 216.0 49.1 m 22.5 w 1.2% 65.9 h 65.1 h INFO 11:49:16,701 ProgressMeter - X:51035366 216.0 50.2 m 23.1 w 1.2% 67.4 h 66.6 h INFO 11:50:24,150 ProgressMeter - X:51035366 216.0 51.3 m 23.6 w 1.2% 68.9 h 68.1 h INFO 11:51:31,883 ProgressMeter - X:51035366 216.0 52.5 m 24.1 w 1.2% 70.5 h 69.6 h INFO 11:52:40,234 ProgressMeter - X:51035366 216.0 53.6 m 24.6 w 1.2% 72.0 h 71.1 h INFO 11:53:46,785 ProgressMeter - X:51035366 216.0 54.7 m 25.1 w 1.2% 73.5 h 72.6 h INFO 11:54:53,194 ProgressMeter - X:51035366 216.0 55.8 m 25.6 w 1.2% 75.0 h 74.0 h

Here is an example of the GVCF for 3 samples in one of the problem haploid regions:

X 51035345 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:7:99:4:0,120 .:2:78:2:0,78 .:9:99:3:0,112 X 51035346 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:7:99:4:0,120 .:2:45:2:0,45 .:9:99:3:0,112 X 51035347 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:7:99:4:0,120 .:2:45:2:0,45 .:9:99:3:0,112 X 51035348 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:7:99:4:0,120 .:2:45:2:0,45 .:9:99:3:0,112 X 51035349 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:7:99:4:0,120 .:2:45:2:0,45 .:9:99:3:0,112 X 51035350 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:7:99:4:0,120 .:2:45:2:0,45 .:9:99:3:0,112 X 51035351 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:7:99:4:0,120 .:2:45:2:0,45 .:9:99:3:0,112 X 51035352 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:7:99:4:0,120 .:2:45:2:0,45 .:9:99:3:0,112 X 51035353 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:7:99:4:0,120 .:2:45:2:0,45 .:9:99:3:0,112 X 51035354 . T <NON_REF> . . END=51035355 GT:DP:GQ:MIN_DP:PL .:7:99:4:0,120 .:2:45:2:0,45 .:9:99:3:0,112 X 51035356 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:7:99:4:0,120 .:1:41:1:0,41 .:9:99:3:0,112 X 51035357 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:7:99:4:0,120 .:1:40:1:0,40 .:9:99:3:0,112 X 51035358 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:7:99:4:0,120 .:1:39:1:0,39 .:9:99:3:0,112 X 51035359 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:7:99:4:0,120 .:1:38:1:0,38 .:9:99:3:0,112 X 51035360 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:7:99:4:0,120 .:1:41:1:0,41 .:9:99:3:0,112 X 51035361 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:7:99:4:0,120 .:1:39:1:0,39 .:9:99:3:0,112 X 51035362 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:7:99:4:0,120 .:1:38:1:0,38 .:9:99:3:0,112 X 51035363 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:7:99:4:0,120 .:1:38:1:0,38 .:9:99:3:0,112 X 51035364 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:4:90:4:0,90 .:1:38:1:0,38 .:9:99:3:0,112 X 51035365 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:4:90:4:0,90 .:2:72:2:0,72 .:9:99:3:0,112 X 51035366 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:4:90:4:0,90 .:2:72:2:0,72 .:9:99:3:0,112 X 51035367 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:4:90:4:0,90 .:2:72:2:0,72 .:9:99:3:0,112 X 51035368 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:4:90:4:0,90 .:2:72:2:0,72 .:9:99:3:0,112 X 51035369 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:4:90:4:0,90 .:2:72:2:0,72 .:9:99:3:0,112 X 51035370 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:4:90:4:0,90 .:2:72:2:0,72 .:9:99:3:0,112 X 51035371 . A C,<NON_REF> . . DP=246;MQ=60.00 GT:AD:DP:GQ:MIN_DP:PL:SB .:0,4,0:4:99:.:126,0,126:0,0,1,3 .:.:2:72:2:0,72,72 .:.:9:99:3:0,112,112 X 51035372 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:4:90:4:0,90 .:2:72:2:0,72 .:9:99:3:0,112 X 51035373 . C <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:4:90:4:0,90 .:2:72:2:0,72 .:9:99:3:0,112 X 51035374 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:2:45:2:0,45 .:2:72:2:0,72 .:9:99:3:0,112 X 51035375 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:2:45:2:0,45 .:2:72:2:0,72 .:9:99:3:0,112 X 51035376 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:2:45:2:0,45 .:2:54:2:0,54 .:9:99:3:0,112 X 51035377 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:2:45:2:0,45 .:2:71:2:0,71 .:9:99:3:0,112 X 51035378 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:18:99:3:0,105 .:2:71:2:0,71 .:9:99:3:0,112 X 51035379 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:18:99:3:0,105 .:2:81:2:0,81 .:9:99:3:0,112 X 51035380 . G <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:18:99:3:0,105 .:2:78:2:0,78 .:9:99:3:0,112 X 51035381 . A <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:18:99:3:0,105 .:2:45:2:0,45 .:9:99:3:0,112 X 51035382 . T <NON_REF> . . . GT:DP:GQ:MIN_DP:PL .:18:99:3:0,105 .:2:45:2:0,45 .:9:99:3:0,112

Any help is greatly appreciated. Please let me know if you need any other information.

Kindest regards, Chris

Created 2015-04-30 06:34:42 | Updated 2015-05-01 15:02:14 | Tags: unifiedgenotyper ploidy queue

Hi, I have several questions about the function "UnifiedGenotyper" and its corresponding Qscript.

1. I first test this function on a single chromosome of my chicken sample (bam file is about 800M) to call SNPs, and set the ploidy value to 30. It took me half a day to finish. Is it normal that it took so long for a single chromosome?

As a result of this, I tried to use the scatter-gather to parallel my job in order to get the full use of my multi-node server. I built my own script based on modifying the ExampleUnifiedGenotyper.scala. I defined "ploidy" as an argument in my Qscript, then I assign a value of 30 to ploidy in my bash command line.

java -Djava.io.tmpdir=$tmp_dir \ -jar /sw/apps/bioinfo/GATK-Queue/3.2.2/Queue.jar \ -S /path/to/ug.scala \ -R$ref_file \
-I /path/to/bamfile.bam \
-o /path/to/my.vcf  \
-ploidy 30 \
-run

2.The script ran successfully, but the output VCF file was based sample_ploidy=2. It seems that it does not respond to the argument "ploidy". Then if I add one command line in the def script() part, which is" genotyper.sample_ploidy = qscript.sample_ploidy ". GATK will give warning of errors "sample_ploidy is not a member of TestUnifiedGenotyper.this.UnifiedGenotyperArguments". Could you please help point out where I did wrong?

Also, I have some questions about how to assign values to argument such as " this.memoryLimit" and "genotyper.scatterCount".

1. Based on the explanation given in the example scala file, argument "this.memoryLimit" sets the memory limit for each command. So in my case, I have only one command in my script, so that I can assign as much memory as I have to it? I am running on a server that has multiple-node, each node with 16 cores, and each core has 8G RAM. So in my understanding, if I run this job on one node with 16 cores, can I assign "this.memoryLimit=128" (16*8)? Do I understand correctly?

2. about the scatterCount, can I assign it with the number of cores I have in the server? That is, based on the example I listed above, 16.

Thank you very much for your help and time! Attached is my Qscript in relating with my question.

My Qscript is as follows:

package org.broadinstitute.gatk.queue.qscripts.examples

class TestUnifiedGenotyper extends QScript {
qscript =>
@Input(doc="The reference file for the bam files.", shortName="R")
var referenceFile: File = _

@Input(doc="Bam file to genotype.", shortName="o")
var outputFile: File = _

@Input(doc="Bam file to genotype.", shortName="I")
var bamFile: File = _

@Input(doc="An optional file with dbSNP information.", shortName="D", required=false)
var dbsnp: File = _

@Argument(doc="Ploidy (number of chromosomes) per sample.", shortName="ploidy")
var sample_ploidy: List[String] = Nil

trait UnifiedGenotyperArguments extends CommandLineGATK {
this.reference_sequence = qscript.referenceFile
this.memoryLimit = 2
}

def script() {
val genotyper = new UnifiedGenotyper with UnifiedGenotyperArguments

genotyper.scatterCount = 3
genotyper.input_file :+= qscript.bamFile
// genotyper.sample_ploidy = qscript.sample_ploidy
genotyper.out = swapExt(outputFile, qscript.bamFile, "bam", "unfiltered.vcf")

}
}

Created 2015-02-19 22:47:05 | Updated | Tags: unifiedgenotyper ploidy vcf

Hi, I'm running on the Unified Genotyper (Version=3.3-0-g37228af) on a pooled sample. The ploidy is set to 32. I'm trying to get allele frequency information. I'm trying to filter sites based on depth of coverage but the DP flag is not consistent within a loci

The DP at the start says there is a depth of 37, but at the end it says its 13. Judging from neighbouring sites, the actual depth seems to be 37, but I'm confused why it seems to only be using 13 of them. At other sites the scores match.

Created 2015-02-02 10:18:45 | Updated | Tags: haplotypecaller ploidy

Hi,

I have a number of samples that consist of multiple individuals from the same population pooled together, and have been truing to use HaplotypeCaller to call the variants. I have set the (ploidy to 2 * number of individuals) but keep getting the same or similar error message, after running for several hours or days:

##### ERROR ------------------------------------------------------------------------------------------

and I'm not sure what I can do to rectify it... Obviously I can't limit the ploidy, it is what it is, and I thought that HC only allows a maximum of six alleles anyway?

My code is below, and any help would be appreciated.

java -Xmx24g -jar ~/bin/GenomeAnalysisTK-3.3-0/GenomeAnalysisTK.jar -T HaplotypeCaller -nct 6 \ -R ~/my_ref_sequence \ --intervals ~/my_intervals_file \ -ploidy 180 \ -log my_log_file \ -I ~/my_input_bam \ -o ~/my_output_vcf

Created 2014-12-15 10:17:16 | Updated | Tags: ploidy genotypegvcfs

Hello. I've run Haplotype caller for 19 samples in -ploidy 19 (19 is as high as I can get without getting an error for that, but that is a discussion opened elsewhere). Then, I've tried GenotypeGVCFs and get an ERROR (both command and ERROR below).

Just to add, I've run both HaplotypeCaller and GenotypeGVCFs with and without -maxAltAlleles 4 to try to limit the referred combination; however, the output is exactly the same ERROR message at the end of GenotypeGVCFs. Do you think there might be a bug or am I doing something wrong?

java -Djava.io.tmpdir=$mytmp -Xmx28g -jar GenomeAnalysisTK.jar -R$ref -T GenotypeGVCFs -o gVCF.ploidy.vcf -V ploidy.list -ploidy 19 -maxAltAlleles 4 ERROR MESSAGE: the combination of ploidy (19) and number of alleles (21) results in a very large number of genotypes (> 2147483647). You need to limit ploidy or the number of alternative alleles to analyz e this locus Created 2014-11-13 17:04:14 | Updated | Tags: ploidy Dear GATK team, We want to know your recommendation as to what variant caller to use if the number of individuals (i.e. ploidy) is unknown, it can be one or many. Our bam files have human amplicons. Any help would be appreciated. Thanks. Created 2014-10-17 12:06:39 | Updated | Tags: haplotypecaller ploidy I am trying to use the HaplotypeCaller with a ploidy setting of 1 to genotype sex chromosomes in a single individual using the following command: java -Xmx4g -jar ~/applications/GenomeAnalysisTK-3.2-2.jar -T HaplotypeCaller -R /data/genome_references/Hmel1-1_primaryScaffolds_mtDNA.fasta -L Z_chromosome.intervals -ploidy 1 -ERC GVCF -variant_index_type LINEAR -variant_index_parameter 128000 -I realigned09-201_Hel_par_ser_HEL_4_CGATGT_L005.bam -hets 0.01 -indelHeterozygosity 0.01 -out_mode EMIT_ALL_CONFIDENT_SITES -maxAltAlleles 1 -o realigned09-201_Hel_par_ser_HEL_4_CGATGT_L005.HC_sex.vcf This is failing. Error message at the bottom. Setting ploidy to 2 works fine. The following command with the UnifiedGeonotyper is also fine: java -Xmx4g -jar ~/applications/GenomeAnalysisTK-3.2-2.jar -T UnifiedGenotyper -R /data/genome_references/Hmel1-1_primaryScaffolds_mtDNA.fasta -ploidy 1 -L Z_chromosome.intervals -I realigned09-201_Hel_par_ser_HEL_4_CGATGT_L005.bam -glm BOTH -hets 0.01 -indelHeterozygosity 0.01 -out_mode EMIT_ALL_CONFIDENT_SITES -o realigned09-201_Hel_par_ser_HEL_4_CGATGT_L005.HC_sex.vcf Any ideas what the problem is? Thanks, Kanchon INFO 12:42:20,180 AFCalcFactory - Requested ploidy 1 maxAltAlleles 6 not supported by requested model EXACT_INDEPENDENT looking for an option INFO 12:42:20,181 AFCalcFactory - Selecting model EXACT_GENERAL_PLOIDY INFO 12:42:21,550 GATKRunReport - Uploaded run statistics report to AWS S3 ##### ERROR ------------------------------------------------------------------------------------------ ##### ERROR stack trace java.lang.NullPointerException at org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.GeneralPloidyExactAFCalc.assignGenotype(GeneralPloidyExactAFCalc.java:559) at org.broadinstitute.gatk.tools.walkers.genotyper.afcalc.GeneralPloidyExactAFCalc.subsetAlleles(GeneralPloidyExactAFCalc.java:527) at org.broadinstitute.gatk.tools.walkers.genotyper.GenotypingEngine.calculateGenotypes(GenotypingEngine.java:286) at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:335) at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:320) at org.broadinstitute.gatk.tools.walkers.genotyper.UnifiedGenotypingEngine.calculateGenotypes(UnifiedGenotypingEngine.java:310) at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.isActive(HaplotypeCaller.java:844) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.addIsActiveResult(TraverseActiveRegions.java:618) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.access800(TraverseActiveRegions.java:78) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$ActiveRegionIterator.hasNext(TraverseActiveRegions.java:378) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.executeSingleThreaded(NanoScheduler.java:268) at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler.execute(NanoScheduler.java:245) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:273) at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions.traverse(TraverseActiveRegions.java:78) at org.broadinstitute.gatk.engine.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:99) at org.broadinstitute.gatk.engine.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:314) at org.broadinstitute.gatk.engine.CommandLineExecutable.execute(CommandLineExecutable.java:121) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:248) at org.broadinstitute.gatk.utils.commandline.CommandLineProgram.start(CommandLineProgram.java:155) at org.broadinstitute.gatk.engine.CommandLineGATK.main(CommandLineGATK.java:107) ##### ERROR ------------------------------------------------------------------------------------------ Created 2014-09-23 22:46:46 | Updated | Tags: unifiedgenotyper ploidy Now that GATK supports ploidy, how do people generate ChrX calls. My first guess is to have 2 separate genotyping runs, one for males with ploidy=1 and a second for females only with ploidy=2? Created 2014-09-11 13:38:40 | Updated | Tags: unifiedgenotyper ploidy multiallelic pooled-calls Hi, Is GATK Unified genotyper able to call multi-allelic positions in a single pooled sample? Case is a pool of 13 samples, we use UG with ploidy set to 26. If I understand the supplementaries of the original publications correct, UG will never be able to call three alleles at a single position. in single sample calling. Or does this not hold for high ploidy analysis? If needed, we can call multiple pools together, but this becomes computationally intensive. In summary, we would like to call a 14xG,6xA,6xT call for example. Also, how does UG take noise into account when genotyping (sequencing errors), when for example 3% of reads is aberrant at a position, this could correspond to ~ 1/26. Thanks for any guidelines, geert Created 2014-04-27 19:07:58 | Updated | Tags: ploidy Hello! I have RNAseq data from 40 insects with a haplodiploid sex determination system. While for pupae and adults I know the sex of the individuals, I would like to determine the sex of the younger life stages. I believe there should be a way to use SNP variants to determine whether a particular library is from a haploid (male) or diploid (female) individual, but I don't know how the GATK tools work and what would be most appropriate. I would appreciate any advice! Created 2014-04-25 14:33:14 | Updated | Tags: ploidy population-samples I am working on population samples from fungi. I am aware that the Haplotype Caller is specific for diploid genomes and the UnifiedGenotyper is preferred for population samples. According to the best practices, I would what like to know what -ploidy should be specified while calling variants of population samples? Created 2014-02-11 02:58:14 | Updated | Tags: unifiedgenotyper ploidy vcf I using the UnifiedGenotyper to call SNPs in a pooled sample of 30 diploid individuals (i.e., I am setting the ploidy to 60). Does this mean that if the coverage is < 60 at a given variant site, the vcf file will read "./." for all alleles at that site? In other words, does it require the coverage to be >= the ploidy or it won't produce a called variant at that site? I'm just trying to make sure I am interpreting the vcf file correctly, in that: if there is a called genotype at a given variant site that I can interpret that as the estimated allele frequency in that pool. Thanks in advance for any advice. Best, Jon Created 2014-01-28 18:29:03 | Updated | Tags: unifiedgenotyper ploidy scala Hi all, I am running a scala script, and would like to the include "-ploidy 1". Any advice on how can I do this? Some information that may or may not be relevant (idk!): I am attempting this using UnifiedGenotyper (v2.7-4). At the top of the script I have: package org.broadinstitute.sting.queue.qscripts.examples import org.broadinstitute.sting.queue.QScript import org.broadinstitute.sting.queue.extensions.gatk._ I got the glm both to work using: genotyper.glm = org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel.Model.BOTH I was hoping for something similar for ploidy. Thanks, Rhys Created 2013-11-04 16:51:48 | Updated | Tags: ploidy Dear Team, Thank you for GATK, which I am learning to use and already considering a great tool. I am trying to analyze a whole genome shotgun dataset from Plasmodium species and trying to decide what ploidy I should use. My dataset comes from a human blood sample. Plasmodia have a brief sexual stage in the mosquito (diploid phase), but then reproduce asexually in the blood of the mammal host (haploid phase). Of course, if the diploid organisms was heterozygous for a certain trait, we are going to have a heterozygous population in the mammalian host. Also, multiclonal infections are possible, it means that more than 2 alleles for the same trait may be present in the blood. I am sorry for the novice question, what would you suggest me regarding the ploidy parameter? Thanks for your time and attention, Kind Regards, Max Created 2013-07-30 09:04:36 | Updated | Tags: unifiedgenotyper ploidy haploid Hi, Just wanted to confirm.. I have a data from 4 spores of a yeast (haploid) tetrad.. If I want to call out variants using all 4 spores (4 bam files), do I need to set -ploidy as 1 or as 4 (Number of samples in each pool * Sample Ploidy) ?? This is the code I am using: java -d64 -Xms1g -Xmx4g -jar GenomeAnalysisTK.jar -glm SNP -nt 52 -R genome.fasta -T UnifiedGenotyper -I$basename"_A.realigned.bam" -I basename"_B.realigned.bam" -Ibasename"_C.realigned.bam" -I basename"_D.realigned.bam" -ploidy 4 -obasename.snps.vcf -stand_call_conf 25.0 -stand_emit_conf 10.0

Thank you.

Created 2013-06-22 19:41:05 | Updated | Tags: ploidy

Hi,

I have three pools of hiseq data where N=20,20, & 40 individuals per pool. I sequenced to ~10x depth for each pool. I would like to use the ploidy setting to estimate probable genotypes from each pool, but I'm torn because it doesn't seem correct to estimate 20 or 40 genotypes from pools that have only been sequenced to 10x depth (only 10 chromosomes could have been sampled). So in such a case, would it be more advisable to set the ploidy level to the depth level of 10 and estimate 5 genotypes per pool?

Thank you very much!

Created 2013-03-12 15:49:44 | Updated | Tags: unifiedgenotyper ploidy

Thank you for developing a great set of tools and adding in the ploidy option to the UnifiedGenotyper! My question is in regards to the ploidy argument when calling multiple pooled samples together. If I have pooled samples from the same population at different time points and want to call SNPs with multiple sample awareness, do I use the ploidy of one sample or that of all samples. For example, if I have pooled samples of approximately 25 haploid genomes each from three different time points from the same population should I use 25 or 75 as my ploidy?

Created 2013-02-07 11:05:27 | Updated 2013-02-08 20:22:14 | Tags: haplotypecaller ploidy

I'm trying to run HaplotypeCaller on a haploid organism. Is this possible? What argument should I use for this? My first attempt produced a diploid calls.

Sorry for the silly question

Created 2012-10-19 17:05:42 | Updated 2012-10-19 17:05:42 | Tags: ploidy

Hi,

I just want to know what you mean by "-ploidy" in UnifiedGenotyper.

--sample_ploidy / -ploidy ( int with default value 2 ) Ploidy (number of chromosomes) per sample. For pooled data, set to (Number of samples in each pool * Sample Ploidy).

I am working on an inbred (homozygous) strain of mice. I have only one sample. Should I use number 2 here that represents the diploid nature of the genome. I am confused as it says Ploidy (number of chromosomes) per sample.

Thanks

Created 2012-10-09 08:55:40 | Updated 2012-10-18 01:03:55 | Tags: unifiedgenotyper ploidy

I am experiencing a problem with the ploidy 1 option. Having used GATK2 unified genotyper with the params --sample_ploidy 1 --genotype_likelihoods_model BOTH -rf BadCigar I get the following line in a vcf file (see sample in bold)

Staphylococcus 1553115 . A G 24454.01 . AC=13;AF=0.813;AN=16;BaseQRankSum=1.072;DP=1040;Dels=0.00;FS=32.822;HaplotypeScore=3.3463;MLEAC=13;MLEAF=0.813;MQ=40.20;MQ0=47;MQRankSum=-10.543;QD=32.13;ReadPosRankSum=-1.148;SB=-9.076e+03 GT:AD:DP:GQ:MLPSAC:MLPSAF:PL 1:0,29:29:99:1:1.00:1015,0 1:0,62:62:99:1:1.00:2053,0 1:0,106:106:99:1:1.00:3210,0 1:0,102:102:99:1:1.00:3305,0 1:0,88:88:99:1:1.00:2750,0 1:0,41:41:99:1:1.00:1324,0 1:0,76:76:99:1:1.00:2448,0 1:0,39:39:99:1:1.00:1303,0 0:64,40:104:99:0:0.00:0,1334 1:0,41:41:99:1:1.00:1373,0 1:0,49:49:99:1:1.00:1668,0 0:72,50:122:99:0:0.00:0,1258 1:0,59:59:99:1:1.00:1852,0 1:0,38:38:99:1:1.00:1192,0 1:0,31:31:99:1:1.00:961,0 0:53,0:53:99:0:0.00:0,1633

The sample in bold is called as WT (genotype 0) with a high GQ despite there being 72 reads of genotype 0 and 50 of genotype 1. Examining the bam file suggests that this is a mapping error in a repetitive phage region

If I set ploidy to be 2 the equivalent line in the resulting vcf file is

Staphylococcus 1553115 . A G 24788.02 . AC=28;AF=0.875;AN=32;BaseQRankSum=0.947;DP=1040;Dels=0.00;FS=32.822;HaplotypeScore=3.3463;InbreedingCoeff=0.4286;MLEAC=28;MLEAF=0.875;MQ=40.20;MQ0=47;MQRankSum=-10.096;QD=25.11;ReadPosRankSum=-1.177;SB=-9.871e+03 GT:AD:DP:GQ:PL 1/1:0,29:29:81:986,81,0 1/1:0,62:62:99:1895,156,0 1/1:0,106:106:99:2992,247,0 1/1:0,102:102:99:3169,268,0 1/1:0,88:88:99:2452,193,0 1/1:0,41:41:99:1243,99,0 1/1:0,76:76:99:2283,193,0 1/1:0,39:39:99:1233,105,0 0/1:64,40:104:99:886,0,1706 1/1:0,41:41:99:1298,108,0 1/1:0,49:49:99:1581,129,0 0/1:72,50:122:99:1235,0,2126 1/1:0,59:59:99:1649,132,0 1/1:0,38:38:87:1065,87,0 1/1:0,31:31:69:821,69,0 0/0:53,0:53:99:0,138,1588

As can be seen from the bold text, the same position is called as heterozygote which based on the number of the reads mapping would be likley except for the fact this is a bacterial haploid genome. Previously I would have discarded this since the heterozygous call indicates mis-mapping as the bam file confirms. I had been hoping to use the sample_polidy option set to 1 for bacterial genomes but this result concerns me. I could obviously filter based on AD but the wonder why the sample was given a high GQ when the polidy is set to 1 and the AD suggests the call of genotype 0 should be doubted.

Any suggestions on what is going on here?? Many thanks

Anthony

Anthony

Created 2012-10-01 16:29:36 | Updated 2012-10-01 17:06:04 | Tags: ploidy haploid

Hello,

Does the GATK team have any recommendations for filtering SNP data for haploid genomes? Our team works with microbial eukaryotes, both haploid and diploid and we have used the GATK v3 best practices for filtering for the latter. [VQSR was not possible, since we do not have access to a truth/high confidence SNP set.]

Thanks, Mika

Created 2012-09-07 00:39:58 | Updated 2012-10-18 01:07:25 | Tags: haplotypecaller ploidy

Hello, I am running the variant caller to identify SNPs and Reference Calls in a bacterial genome, which means I am running with -ploidy 1, -glm POOLSNP and -prnm POOL as suggested in other regions of this forum. The tool does an excellent job when just looking for Variants, but when I attempt to EMIT_ALL_CONFIDENT_SITES, it just spits out the SNPs and not the reference calls. When I remove the arguments stating that it is ploidy of 1, it works fine but calls SNPs that shouldn't be there since it's assuming diploid. Thus, I would really like to be able to emit all sites in ploidy=1 mode. Any reason why this is not possible? Thanks for you help! John

Created 2012-07-24 06:49:35 | Updated 2012-07-24 13:04:31 | Tags: unifiedgenotyper ploidy snp

Leishmania has 36 chromosomes but their copy number is unpredictable for each strain and chromosome copy number can change very quickly. So what is an optimal ploidy setting for organisms with extensive aneuploidy? So far we use just diploid setting. Some samples have consistently more heterozygous SNPs in higher copy chromosomes but this relationship does not hold in many other samples: there is no strong correlation between chromosome copy number and abundance of heterozygous SNPs.