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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 .
When the callers emit sites, they specify whether the variant qual score is above the call confidence threshold (no filter, hence ".") or under it (hence "Low Qual"). Because it is a sort of pre-filtering but not real filtering, called sites don't get marked PASS. Does that clarify things?
Geraldine Van der Auwera, PhD
It simply means no filtering has been applied to the variants.
why did that happen? there are filters, such as low qual, in some other sites.
22 16084135 . A T 42.77 LowQual
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 \
Also since "." means above the call confidence threshold, how to change it to PASS? Thanks!
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.