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VariantsToTable - acces to BaseQRankSum or similar stats

rwaplesrwaples Seattle, WAPosts: 3Member

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

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  • rwaplesrwaples Seattle, WAPosts: 3Member
    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

    Post edited by rwaples on
  • rwaplesrwaples Seattle, WAPosts: 3Member

    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 Posts: 5,869Administrator, GATK Developer 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.

    Geraldine Van der Auwera, PhD

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