Tagged with #variantstotable
1 documentation article | 0 announcements | 8 forum discussions


Comments (2)

A new tool has been released!

Check out the documentation at VariantsToTable.

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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

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!

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!

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

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

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

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
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