Difference between and strict_strand strand bias in vcf files generated by FilterMutectCalls

Follow

Leo Hsiao

• April 24, 2020 12:11

a) GATK version used: 4.1.5.0 and 4.1.6.0

b) Exact GATK commands used: FilterMutectCalls

c) When I look at the output vcf files generated by FilterMutectCalls, I found it's a little confusing to me.

Based on the header, two filters related to strand bias looks pretty similar. Does anyone know what's the difference there?

##FILTER=<ID=strand_bias,Description="Evidence for alt allele comes from one read direction only">
##FILTER=<ID=strict_strand,Description="Evidence for alt allele is not represented in both directions">

Thank you !

0

• 

  David Benjamin

  • May 04, 2020 21:09

  Leo Hsiao The strict strand bias filter is only used for the Broad's duplex sequencing pipeline or similar applications with an extreme preference for precision at the expense of sensitivity.  It is inactive by default, though it shows up in the VCF header.  Just continue to run FilterMutectCalls with default settings and this extra filter won't cause any trouble.

  0

  Comment actions Permalink

Please sign in to leave a comment.