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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

    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.

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