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# FILTER column in vcf file from HaplotypeCaller

Posts: 194Member

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  .

Tagged:

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

Geraldine Van der Auwera, PhD

• Posts: 194Member

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

22 16084135 . A T 42.77 LowQual

• Posts: 194Member

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

• Posts: 194Member

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