Tagged with #variantstotable
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Created 2012-07-23 23:57:17 | Updated 2012-07-23 23:57:17 | Tags: variantstotable gatkdocs
Comments (2)

A new tool has been released!

Check out the documentation at VariantsToTable.

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Created 2015-08-04 19:11:47 | Updated | Tags: selectvariants variantstotable
Comments (4)

Hello GATK team,

Given a sample.txt file to be used with -sf flag, and sample names given on each line, is there an option in SelectVariants and/or VariantsToTable that allows output to be ordered as specified?

sample.txt file: Ind1 Ind4 Ind2 Ind3

desired sample fields in .vcf file: Ind1 Ind4 Ind2 Ind3

This can be done with command line tools, but thought I would ask here first. Thanks!


Created 2015-05-29 12:53:42 | Updated | Tags: variantstotable
Comments (3)

Hi there,

When using the VariantsToTable function, is there a way to force the genotypes to be numeric, i.e. 0/1 or 0/0 rather than the actual bases like G/T, G/G, etc.? I can't seem to find anything in the tool documentation, but maybe there's another way.

Thanks, Steve


Created 2015-03-02 05:53:27 | Updated 2015-03-02 05:54:21 | Tags: variantstotable vcf multi-sample
Comments (4)

Hi-

Will VariantsToTable work for multi-sample VCF files? I've tried the following command, but it only outputs the column headers:

java -jar ~/tools/GenomeAnalysisTK.jar -R chr1.fa -T VariantsToTable -V cg_100.vcf.gz -F CHROM -F POS -F ID -F REF -F ALT -F F-101-009 -o test.table

Thanks, Summer


Created 2014-12-05 10:47:36 | Updated | Tags: variantstotable 3-3-0 2-7-1
Comments (14)

Hi Team,

When asking VariantsToTable to return `-GF AD` and `-GF PL`, these fields are represented in the outfile as '[[I@7e1b96a7]', '[[I@29c8a858]', etc. This appears to be limited to multi-allelic variants, and happens with versions 3.3-0, 3.3-3, 3.1-1, and 2.7-1.

Is this expected behaviour, and if yes, is there a way to 'decode' [[I@49c72461]?

Many thanks in advance, and thanks for the great tools!


Created 2014-11-10 16:55:43 | Updated | Tags: variantstotable
Comments (3)

Hi

I just started using VariantsToTable tool, which works great. I am still facing a problem with genotype fields extracted from vcf as the numbered genotypes (0/1) are changed to nucleotides (T/C). That is something that I do not want. Therefore, I would like to ask, if there is a way to stop this happening, so that the walker leaves genotypes to number format as they are in vcf file?

Thank you!


Created 2014-11-05 15:17:17 | Updated | Tags: variantstotable
Comments (2)

Hi,

I am using the VariantsToTable walker to convert my vcfs to tabular format. Previously I have done same filtering with vcftools in my vcfs input files. VariantsToTable walker output file only contains just a few of the SNPs I have in my input file. Specifically, those which have the tag "PASS" in FILTER column. I need a table with all the input SNPs, regardless FILTER column value. Is there any way to do it?

Thanks


Created 2013-11-06 13:41:46 | Updated | Tags: variantstotable
Comments (8)

Hi,

I am using the VariantsToTable walker to convert my vcfs to tabular format. However, I keep getting the following error:

Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types

The problem is that I don't understand what is meant by the advice. How do you actually provide the :NAME tag in the command line - I have tried a number of ways and nothing seems to work and I can't find any reference to this tag in the documentation.

Best wishes,

Kath


Created 2013-10-09 23:24:28 | Updated | Tags: variantstotable
Comments (4)

I'm having trouble accessing the INFO field "BaseQRankSum" when using VariantsToTable.

I cannot seem to acces this info. Other fields such as CHROM POS DP HET or even -GT fields work fine.

Example cmd line: java -jar /home/ipseg/Programs/GATK/GenomeAnalysisTK-2.7-2-g6bda569/GenomeAnalysisTK.jar \ -T VariantsToTable \ -R '/olympus/DATA/PROJECTS/SNP DISCOVERY/EXOME CAPTURE/bowtie2/reference/cap3_contigs.fa' \ -V '/home/ipseg/Desktop/TEMP/GATK/variants.vcf' \ -F BaseQRankSum \ -o '/olympus/DATA/PROJECTS/SNP DISCOVERY/EXOME CAPTURE/bwa/GATK/CAGATC_table.tsv' \ --allowMissingData

Every line is NA


Created 2013-08-29 21:40:26 | Updated 2013-09-04 22:57:55 | Tags: variantstotable
Comments (9)

Hi, I have a vcf file that I have annotated dbsnp id and cosmic id in the ID field (GATK -> vcf ->VariantAnnotator to append COSMIC ids in to the id field already populated with dbsnpid.I want this way for whatever reason.) When I use such vcf (with appended ids) as an --variant argumet with VariantToTable - first of all it complains about Tribble not beeing supplied - so I would tweak in the command as --variant:vcf,<input.vcf> it works but empty output.

When I supply regular vcf spitted out by GATK,it runs fanstastic. Can somebody change this behaviour? or do I get a source code that I can tweak to get this going for the vcf format I want? Thx.

with regular vcf file

$ java -jar  GenomeAnalysisTK-2.5-2-gf57256b/GenomeAnalysisTK.jar -R  hg19.masked.fasta -T VariantsToTable --variant input.sorted.vcf -o table  -F CHROM -F POS -F REF -F ALT -F ID -F QUAL -F MQ -F DP -F AF -F AD -AMD
INFO  16:46:44,633 HelpFormatter - --------------------------------------------------------------------------------
INFO  16:46:44,635 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.5-2-gf57256b, Compiled 2013/05/01 09:27:02
INFO  16:46:44,635 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  16:46:44,635 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  16:46:44,637 HelpFormatter - Program Args: -R  -R  hg19.masked.fasta -T VariantsToTable --variant input.sorted.vcf -o table  -F CHROM -F POS -F REF -F ALT -F ID -F QUAL -F MQ -F DP -F AF -F AD -AMD
INFO  16:46:44,637 HelpFormatter - Date/Time: 2013/08/29 16:46:44
INFO  16:46:44,637 HelpFormatter - --------------------------------------------------------------------------------
INFO  16:46:44,637 HelpFormatter - --------------------------------------------------------------------------------
INFO  16:46:44,642 ArgumentTypeDescriptor - Dynamically determined type of input.sorted.vcf to be VCF
INFO  16:46:44,672 GenomeAnalysisEngine - Strictness is SILENT
INFO  16:46:44,713 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO  16:46:44,727 RMDTrackBuilder - Loading Tribble index from disk for file input.sorted.vcf
INFO  16:46:44,861 GenomeAnalysisEngine - Creating shard strategy for 0 BAM files
INFO  16:46:44,870 GenomeAnalysisEngine - Done creating shard strategy
INFO  16:46:44,870 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO  16:46:44,870 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
INFO  16:46:53,708 ProgressMeter -            done        3.46e+05    8.0 s       25.0 s     98.7%         8.0 s     0.0 s
INFO  16:46:53,709 ProgressMeter - Total runtime 8.84 secs, 0.15 min, 0.00 hours
INFO  16:46:54,228 GATKRunReport - Uploaded run statistics report to AWS S3

$ wc -l table
346436 table

$ wc -l input.sorted.vcf
346491 input.sorted.vcf  

~~~~~~~~~~

With altered vcf:

$ java -jar GenomeAnalysisTK.jar -R  hg19.masked.fasta -T VariantsToTable --variant input.sorted.dbsnp-cosmic.vcf -o table  -F CHROM -F POS -F REF -F ALT -F ID -F QUAL -F MQ -F DP -F AF -F AD -AMD

INFO  17:03:55,412 HelpFormatter - --------------------------------------------------------------------------------
INFO  17:03:55,413 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.5-2-gf57256b, Compiled 2013/05/01 09:27:02
INFO  17:03:55,413 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  17:03:55,413 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  17:03:55,416 HelpFormatter - Program Args: -R  hg19.masked.fasta -T VariantsToTable --variant input.sorted.dbsnp-cosmic.vcf -o table  -F CHROM -F POS -F REF -F ALT -F ID -F QUAL -F MQ -F DP -F AF -F AD -AMD
INFO  17:03:55,416 HelpFormatter - Date/Time: 2013/08/29 17:03:55
INFO  17:03:55,416 HelpFormatter - --------------------------------------------------------------------------------
INFO  17:03:55,416 HelpFormatter - --------------------------------------------------------------------------------
INFO  17:03:56,114 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.5-2-gf57256b):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Invalid command line: No tribble type was provided on the command line and the type of the file could not be determined dynamically. Please add an explicit type tag :NAME listing the correct type from among the supported types:
##### ERROR Name      FeatureType   Documentation
##### ERROR BCF2   VariantContext   http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_variant_bcf2_BCF2Codec.html
##### ERROR  VCF   VariantContext   http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_variant_vcf_VCFCodec.html
##### ERROR VCF3   VariantContext   http://www.broadinstitute.org/gatk/gatkdocs/org_broadinstitute_variant_vcf_VCF3Codec.html
##### ERROR ------------------------------------------------------------------------------------------

$ java -jar GenomeAnalysisTK.jar -R hg19.masked.fasta -T VariantsToTable --variant:vcf,input.sorted.dbsnp-cosmic.vcf -o table  -F CHROM -F POS -F REF -F ALT -F ID -F QUAL -F MQ -F DP -F AF -F AD -AMD
INFO  17:04:19,779 HelpFormatter - --------------------------------------------------------------------------------
INFO  17:04:19,781 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.5-2-gf57256b, Compiled 2013/05/01 09:27:02
INFO  17:04:19,781 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO  17:04:19,781 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk
INFO  17:04:19,783 HelpFormatter - Program Args: -R hg19.masked.fasta -T VariantsToTable --variant:vcf,input.sorted.dbsnp-cosmic.vcf -o table  -F CHROM -F POS -F REF -F ALT -F ID -F QUAL -F MQ -F DP -F AF -F AD -AMD
INFO  17:04:19,783 HelpFormatter - Date/Time: 2013/08/29 17:04:19
INFO  17:04:19,784 HelpFormatter - --------------------------------------------------------------------------------
INFO  17:04:19,784 HelpFormatter - --------------------------------------------------------------------------------
INFO  17:04:19,816 GenomeAnalysisEngine - Strictness is SILENT
INFO  17:04:19,858 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000
INFO  17:04:19,898 GenomeAnalysisEngine - Creating shard strategy for 0 BAM files
INFO  17:04:19,908 GenomeAnalysisEngine - Done creating shard strategy
INFO  17:04:19,908 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING]
INFO  17:04:19,908 ProgressMeter -        Location processed.sites  runtime per.1M.sites completed total.runtime remaining
INFO  17:04:20,101 ProgressMeter -            done        0.00e+00    0.0 s       53.3 h    100.0%         0.0 s     0.0 s
INFO  17:04:20,101 ProgressMeter - Total runtime 0.19 secs, 0.00 min, 0.00 hours
INFO  17:04:20,550 GATKRunReport - Uploaded run statistics report to AWS S3

$ wc -l table
1 table

$ cat table
CHROM   POS REF ALT ID  QUAL    MQ  DP  AF  AD

Created 2013-05-20 14:37:20 | Updated | Tags: variantstotable
Comments (9)

Hi,

Can the VariantsToTable walker produce output containing all the fields in the VCF without you having to specify them in the command?

Thanks

Kath