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FILTER column in vcf file from HaplotypeCaller

blueskypyblueskypy Member Posts: 266 ✭✭

I used a cohort in running HaplotypeCaller. Some of values in the FILTER column of the resulting vcf file are ".", what does that mean?

Here is one example (not all columns included):

#CHROM  POS     ID      REF     ALT     QUAL    FILTER
22      16084134        .       A       C       152.03  .

Best Answer


  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,728 admin

    It simply means no filtering has been applied to the variants.

    Geraldine Van der Auwera, PhD

  • blueskypyblueskypy Member Posts: 266 ✭✭

    why did that happen? there are filters, such as low qual, in some other sites.

    22 16084135 . A T 42.77 LowQual

  • blueskypyblueskypy Member Posts: 266 ✭✭

    Does the GenotypeConcordance include those sites with "." under FILTER by the following command?

    java -Xmx4g -jar $gatkDir/GenomeAnalysisTK.jar -T GenotypeConcordance \
     -R $refGenome \
     -comp jpt.ERR034601.chr22.1kg.vcf \
     -eval jpt.ERR034601.j2w45.raw.var.vcf \
     -o jpt.ERR034601.j2w45.vs.1kg.txt
  • blueskypyblueskypy Member Posts: 266 ✭✭

    Also since "." means above the call confidence threshold, how to change it to PASS? Thanks!

  • Geraldine_VdAuweraGeraldine_VdAuwera Cambridge, MAMember, Administrator, Broadie Posts: 11,728 admin

    GenotypeConcordance will use any sites with either "." or "PASS" in the FILTER field. When you filter your variants (either with VariantRecalibrator or VariantFiltration) the "good" variants will get marked "PASS", all others will be marked with the name of the filter that they failed.

    Geraldine Van der Auwera, PhD

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