Tagged with #gatk walkers
92 documentation articles | 0 announcements | 8 forum discussions


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A new tool has been released!

Check out the documentation at Yamagishi.

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A new tool has been released!

Check out the documentation at VariantsToVCF.

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A new tool has been released!

Check out the documentation at VariantsToTable.

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A new tool has been released!

Check out the documentation at VariantsToPED.

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A new tool has been released!

Check out the documentation at VariantAnnotator.

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A new tool has been released!

Check out the documentation at VariantEval.

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A new tool has been released!

Check out the documentation at ValidateVariants.

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A new tool has been released!

Check out the documentation at ValidatingPileup.

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A new tool has been released!

Check out the documentation at ValidateBAQ.

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A new tool has been released!

Check out the documentation at UnifiedGenotyper.

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A new tool has been released!

Check out the documentation at UGCallVariants.

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Check out the documentation at TestReadFishing.

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A new tool has been released!

Check out the documentation at TableToVCF.

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Check out the documentation at SplitSamFile.

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Check out the documentation at SelectVariants.

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Check out the documentation at SelectHeaders.

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Check out the documentation at ScoreSeq.

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Check out the documentation at SNPDensity.

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### This tool is not currently available to the public, sorry.
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A new tool has been released!

Check out the documentation at ReduceReads.

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Check out the documentation at ReadValidation.

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Check out the documentation at QuantizeQuals.

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Check out the documentation at ProfileRodSystem.

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Check out the documentation at QCRef.

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Check out the documentation at PrintReads.

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Check out the documentation at PrintRODs.

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Check out the documentation at Pileup.

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Check out the documentation at LocusMismatch.

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Check out the documentation at LiftoverVariants.

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Check out the documentation at LeftAlignIndels.

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Check out the documentation at InsertRODs.

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Check out the documentation at IndelRealigner.

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Check out the documentation at IOCrusher.

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A new tool has been released!

Check out the documentation at HaplotypeCaller.

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Check out the documentation at FlagStat.

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Check out the documentation at FixGenotypes.

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Check out the documentation at FastaStats.

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A new tool has been released!

Check out the documentation at FastaReference.

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A new tool has been released!

Check out the documentation at CombineVariants.

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A new tool has been released!

Check out the documentation at CGVarToVCF.

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A new tool has been released!

Check out the documentation at BaseRecalibrator.

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Comments (4)

Hi,

I was wondering if there is a nice way to apply multiple processing steps to each variant (or a group of variants) as they are read so that the variant file is not read again and again. My understanding is that even if I use Queue, each script would read the vcf again. Is that correct?

Comments (0)

Hi there,

I've a problem running GATK2.8's VariantRecalibrator, I get Code Exception (java.lang.NullPointerException). Below is the error trace:

INFO 17:05:37,528 GenomeAnalysisEngine - Preparing for traversal INFO 17:14:27,706 VariantDataManager - MQRankSum: mean = -0.09 standard deviation = 0.99 INFO 17:14:27,742 VariantDataManager - ReadPosRankSum: mean = 0.18 standard deviation = 0.96 INFO 17:14:27,820 VariantDataManager - Annotations are now ordered by their information content: [QD, ReadPosRankSum, MQRankSum] INFO 17:14:27,823 VariantDataManager - Training with 2739 variants after standard deviation thresholding. INFO 17:14:27,829 GaussianMixtureModel - Initializing model with 100 k-means iterations... INFO 17:14:28,389 VariantRecalibratorEngine - Finished iteration 0. INFO 17:14:28,534 VariantRecalibratorEngine - Finished iteration 5. Current change in mixture coefficients = 0.20522 INFO 17:14:28,601 VariantRecalibratorEngine - Finished iteration 10. Current change in mixture coefficients = 0.46290 INFO 17:14:28,675 VariantRecalibratorEngine - Finished iteration 15. Current change in mixture coefficients = 9.95604 INFO 17:14:28,759 VariantRecalibratorEngine - Finished iteration 20. Current change in mixture coefficients = 9.00456 INFO 17:14:28,861 VariantRecalibratorEngine - Finished iteration 25. Current change in mixture coefficients = 0.01190 INFO 17:14:28,951 VariantRecalibratorEngine - Finished iteration 30. Current change in mixture coefficients = 0.00796 INFO 17:14:29,041 VariantRecalibratorEngine - Finished iteration 35. Current change in mixture coefficients = 0.00546 INFO 17:14:29,131 VariantRecalibratorEngine - Finished iteration 40. Current change in mixture coefficients = 0.00360 INFO 17:14:29,221 VariantRecalibratorEngine - Finished iteration 45. Current change in mixture coefficients = 0.00218 INFO 17:14:29,239 VariantRecalibratorEngine - Convergence after 46 iterations! INFO 17:14:29,276 VariantRecalibratorEngine - Evaluating full set of 13495 variants... INFO 17:14:29,280 VariantDataManager - Training with worst 0 scoring variants --> variants with LOD <= -5.0000. INFO 17:14:32,024 GATKRunReport - Uploaded run statistics report to AWS S3

ERROR ------------------------------------------------------------------------------------------
ERROR stack trace

java.lang.NullPointerException at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibratorEngine.generateModel(VariantRecalibratorEngine.java:83) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:359) at org.broadinstitute.sting.gatk.walkers.variantrecalibration.VariantRecalibrator.onTraversalDone(VariantRecalibrator.java:139) at org.broadinstitute.sting.gatk.executive.Accumulator$StandardAccumulator.finishTraversal(Accumulator.java:129) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:116) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:313) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:245) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:152) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:91)

ERROR ------------------------------------------------------------------------------------------
ERROR A GATK RUNTIME ERROR has occurred (version 2.8-1-g932cd3a):
ERROR
ERROR This might be a bug. Please check the documentation guide to see if this is a known problem.
ERROR If not, please post the error message, with stack trace, to the GATK forum.
ERROR Visit our website and forum for extensive documentation and answers to
ERROR commonly asked questions http://www.broadinstitute.org/gatk
ERROR
ERROR MESSAGE: Code exception (see stack trace for error itself)
ERROR ------------------------------------------------------------------------------------------

And this is the command i used:

java -XX:+UseParallelGC -XX:ParallelGCThreads=8 -Xmx4g -jar ~/genomekey-data/tools/gatk2.jar -T VariantRecalibrator -R ~/genomekey-data/bwa_references/human_g1k_v37.fasta -input ~/simplex/ngs_test/snp_calling/aln.haplotyper.raw.vcf -resource:dbsnp,known=true,training=false,truth=false,prior=8.0 ~/genomekey-data/bundle/current/dbsnp_137.b37.vcf -resource:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 ~/genomekey-data/bundle/current/hapmap_3.3.b37.vcf -resource:omni,VCF,known=false,training=true,truth=false,prior=12.0 ~/genomekey-data/bundle/current/1000G_omni2.5.b37.vcf -an QD -an MQRankSum -an ReadPosRankSum -recalFile ~/simplex/ngs_test/snp_recal/aln.snp.recal -tranche 100 -tranche 99.9 -tranche 99.0 -tranche 90 -tranchesFile ~/simplex/ngs_test/snp_recal/aln.snp.tranches -rscriptFile ~/simplex/ngs_test/snp_recal/aln.snp.plots.R -mode SNP

Please note that i got the same error running GATK 2.6. Any help or suggestions will be appreciated.

Thanks, Shazly

Comments (7)

Is there anyway to write a sliding window RodWalker? I've been try to look in your documentation, but I have not found a clue.

Comments (2)

Hi guys,

I am working with three genomes from the same species. I have managed to call variants between the reference and two of the genomes but the third seems to be having an issue that I don't know. I processed them exactly in the same pipeline prior to calling the variants on them using HaplotypeCaller. However, on the third genome the algorithm produces an empty vcf file as if it encountered an exact replica of the reference genome. It doesn't seem like its encountering any type of error as the log file shows that it is walking through the genome fine and the standard error file is empty (no error messages)

My code for calling the variants is as follows:

java -Xmx6g -jar Documents/GenomeAnalysisTK-2.6-5-gba531bd/GenomeAnalysisTK.jar -T HaplotypeCaller -nct 4 -R equcab2.fa -I Documents/PhD_work/recal.bam -stand_call_conf 20 -stand_emit_conf 10.0 -o output.raw.snps.indels.vcf 1>> gatk_HaplotypeCaller.log 2>> gatk_HaplotypeCaller.stderr

I would really appreciate if someone can help me out with this.

Thank you! :-)

Comments (3)

I have twice run UnifiedGenotyper and the resultant .vcf file contains only part of chromosome 20. I do not see what I am doing wrong. Neither do the other two people in the lab who have extensive experience with GATKcat

Comments (1)

I am confused about the Command-line Argument, --downsample_to_coverage. How do I know if the walker is "locus-based" or "non-locus-based"? Your on-line guide page gives an example of each but not how to identify one type of walker from another.

Comments (3)

The User Guide on line at this URL
http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_sting_gatk_walkers_genotyper_UnifiedGenotyper.html
has this text
Example command for generating calls at all sites
...
-o my.vcf \
...
--out / -o ( VariantContextWriter with default value stdout )
File to which variants should be written. A raw, unfiltered, highly sensitive callset in VCF format.

In my hands -o my.vcf produces an error message, complaining that there is no --out
while --out my.vcf works without error

Any suggestions?

Comments (5)

Hello,

I try to run the realigner target creator with the data divided on chromosomes. It seems to run smooth but the runtime for chromosome 1 seems to never end. I have checked my bam files and as expected the one with chr 1 is a little bit bigger than chr 2 but nothing proportional to the differences in predicted runtime. The version i use is GATK 2.3.0 and this is how i run it:

java -Xmx12g -jar programs/GenomeAnalysisTK-2.3-0/GenomeAnalysisTK.jar -l INFO -T VariantRecalibrator -R Homo_sapiens.GRCh37.57_dna_concat.fa -recalFile allchr_varrecal_BOTH_comb_ref.intervals -rscriptFile 15_allchr_varrecal_BOTH_comb_ref.intervals.plots.R -tranchesFile allchr_varrecal_BOTH_comb_ref.intervals.tranches -resource:hapmap,VCF,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.b37.sites.vcf -resource:omni,VCF,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.b37.sites.vcf -resource:dbsnp,VCF,known=true,training=false,truth=false,prior=8.0 dbsnp_135.b37.vcf -resource:mills,VCF,known=true,training=true,truth=true,prior=12.0 Mills_and_1000G_gold_standard.indels.hg19.sites.vcf -an QD -an HaplotypeScore -an MQRankSum -an ReadPosRankSum -an FS -an MQ --mode BOTH -nt 8 -input allchr_real_recal_resrt_raw_BOTH_comb_ref.vcf -L Agilent_SureSelect.V4.GRCh37.70_targets_nochr.bed.pad100.interval_list --pedigreeValidationType SILENT --pedigree my_fam.fam

predicted runtime looks like:

INFO 15:11:33,778 ProgressMeter - 1:33587200 3.36e+07 2.3 h 4.1 m 1.1% 8.8 d 8.7 d INFO 15:11:33,778 ProgressMeter - 11:73495886 1.82e+09 2.3 h 4.5 s 61.0% 3.7 h 87.4 m INFO 15:11:33,778 ProgressMeter - 10:6623707 1.68e+09 2.3 h 4.9 s 54.5% 4.2 h 114.3 m INFO 15:11:33,778 ProgressMeter - 11:572298 1.82e+09 2.3 h 4.5 s 58.7% 3.9 h 96.4 m INFO 15:11:33,779 ProgressMeter - 11:122078003 1.82e+09 2.3 h 4.5 s 62.6% 3.6 h 81.7 m INFO 15:11:53,780 ProgressMeter - 11:10589211 1.82e+09 2.3 h 4.5 s 59.0% 3.9 h 95.3 m INFO 15:11:53,780 ProgressMeter - 11:105031869 1.82e+09 2.3 h 4.5 s 62.1% 3.7 h 83.9 m INFO 15:11:53,781 ProgressMeter - 11:46994477 1.82e+09 2.3 h 4.5 s 60.2% 3.8 h 90.8 m INFO 15:12:03,779 ProgressMeter - 11:8677862 1.82e+09 2.3 h 4.5 s 58.9% 3.9 h 95.7 m INFO 15:12:03,779 ProgressMeter - 11:130690257 1.82e+09 2.3 h 4.5 s 62.9% 3.6 h 81.1 m INFO 15:12:13,779 ProgressMeter - 11:84816026 1.82e+09 2.3 h 4.5 s 61.4% 3.7 h 86.4 m INFO 15:12:13,779 ProgressMeter - 10:17039143 1.68e+09 2.3 h 4.9 s 54.8% 4.2 h 113.3 m INFO 15:12:23,780 ProgressMeter - 11:18556991 1.82e+09 2.3 h 4.5 s 59.3% 3.9 h 94.6 m INFO 15:12:23,780 ProgressMeter - 11:113365440 1.82e+09 2.3 h 4.5 s 62.3% 3.7 h 83.2 m INFO 15:12:23,782 ProgressMeter - 11:55284794 1.82e+09 2.3 h 4.5 s 60.4% 3.8 h 90.1 m INFO 15:12:33,780 ProgressMeter - 1:33783808 3.38e+07 2.3 h 4.1 m 1.1% 8.8 d 8.7 d INFO 15:12:33,780 ProgressMeter - 12:3311608 1.95e+09 2.3 h 4.2 s 63.1% 3.6 h 80.5 m INFO 15:12:43,779 ProgressMeter - 11:93292307 1.82e+09 2.3 h 4.6 s 61.7% 3.7 h 85.8 m INFO 15:12:43,780 ProgressMeter - 10:24841443 1.68e+09 2.3 h 4.9 s 55.1% 4.2 h 112.5 m INFO 15:12:43,780 ProgressMeter - 11:19408689 1.82e+09 2.3 h 4.6 s 59.3% 3.9 h 94.8 m INFO 15:12:53,965 ProgressMeter - 11:26512308 1.82e+09 2.3 h 4.6 s 59.5% 3.9 h 94.0 m INFO 15:12:53,965 ProgressMeter - 11:121738354 1.82e+09 2.3 h 4.6 s 62.6% 3.7 h 82.6 m INFO 15:12:53,965 ProgressMeter - 11:63468191 1.82e+09 2.3 h 4.6 s 60.7% 3.8 h 89.4 m INFO 15:13:03,781 ProgressMeter - 12:11960820 1.95e+09 2.3 h 4.3 s 63.4% 3.6 h 79.8 m INFO 15:13:13,780 ProgressMeter - 11:101551879 1.82e+09 2.3 h 4.6 s 61.9% 3.7 h 85.1 m INFO 15:13:13,780 ProgressMeter - 10:32238974 1.68e+09 2.3 h 4.9 s 55.3% 4.2 h 111.8 m INFO 15:13:13,780 ProgressMeter - 11:27204534 1.82e+09 2.3 h 4.6 s 59.5% 3.9 h 94.1 m INFO 15:13:23,966 ProgressMeter - 11:71529440 1.82e+09 2.3 h 4.6 s 61.0% 3.8 h 88.8 m INFO 15:13:23,968 ProgressMeter - 11:34170083 1.82e+09 2.3 h 4.6 s 59.8% 3.9 h 93.4 m INFO 15:13:23,977 ProgressMeter - 11:129889715 1.82e+09 2.3 h 4.6 s 62.9% 3.7 h 81.9 m INFO 15:13:33,781 ProgressMeter - 1:33980416 3.40e+07 2.3 h 4.1 m 1.1% 8.8 d 8.7 d

Any suggestions?

Regards,

Måns