Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Attention:
We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.

VariantsToTable - acces to BaseQRankSum or similar stats

rwaplesrwaples Seattle, WAMember

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

Tagged:

Best Answer

Answers

  • rwaplesrwaples Seattle, WAMember
    edited October 2013

    I should note that this vcf was generated by GATK and has the header line:
    INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">

    And I see the field within the VCF.
    Example containing line:

    ONTS_CLUSTER_ID#4216706_1254_1423|Contig1 70 . A T 955.77 . AC=1;AF=0.500;AN=2;BaseQRankSum=-1.510;ClippingRankSum=-0.170;DP=49;FS=1.298;MLEAC=1;MLEAF=0.500;MQ=59.45;MQ0=0;MQRankSum=-0.150;QD=19.51;ReadPosRankSum=-0.850 GT:AD:DP:GQ:PL 0/1:24,25:49:99:984,0,1936

  • rwaplesrwaples Seattle, WAMember

    Ok, this is a little wierd. I subsetted my .vcf file:
    -T SelectVariants \
    -fraction 0.005

    And got down to a few hundred variants (This a salmon exome capture project), re-ran the VariantsToTable with "-F BaseQRankSum" and it worked just fine, i get the BaseQRankSum statistic. Tried again on my full .vcf file with no luck. I tried subsetting with fraction 1.0 (bascially remaking .vcf) and again it worked just fine. I deleted the index file for the full vcf and re-ran VariantsToTable, with success!
    So thanks, but I think this was a once-of error in the index file. If can follow this up any more let me know.

    -ryan

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie admin

    Hi Ryan, that's certainly odd; but if it's working now there's nothing I can really do to follow up. Thanks for reporting back, it's helpful for us to know that this symptom can be cause by an index blip.

Sign In or Register to comment.