Mutect2 : annotation group & fields that can check strand bias

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whynot

• February 20, 2020 08:27

Hi :)

I want to check the strand bias in the vcf file.

 

So I check default annotation (group).

> Mutect2 : Default annotation group = [StandardMutectAnnotation]

> HaplotypeCaller : Default annotation group = [StandardAnnotation, StandardHCAnnotation]

 

I think FOXOG(F1R2, F2R1) is the one to measure strand bias among Mutect2's default annotation variant calling.

also, I think SOR is the one to measure strand bias among HaplotypeCaller's default annotation variant calling, and I checked that SOR is printed on application StandardAnnotation group.

 

I have 2 questions ;

 

Q1 : Why does Mutect2 to StandardAnnotation group not apply by default, and therefore not print SOR?

 

Q2 : Because SOR is not printed by default, I thought I should see FOXOG to check the strand bias of the variant called with Mutect2. Does FOXOG represent strand bias better than SOR when calling with Mutect2? If yes, why?

 

 

 

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  David Benjamin

  • February 24, 2020 03:03

  FOXOG was an orientation bias annotation, which is not quite the same thing as strand bias.  In any case Mutect2 hasn't emitted this annotation for quite a while.  Mutect2's default strand read count annotation is StrandBiasBySample (SB).  FilterMutectCalls contains a strand artifact model that internally calculates the probability that an allele is a strand bias artifact.  In addition to possibly applying a strand bias filter, it applies a STRANDQ annotation denoting the phred-scaled probability that a variant is a strand artifact.

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