Some interpretation of Strelka output

Question

[zizigolu]

Hi

I have called INDELs for tumor/matched normal by Strelka caller

In .vcf header I have

##FORMAT=<ID=TAR,Number=2,Type=Integer,Description="Reads strongly supporting alternate allele for tiers 1,2">
##FORMAT=<ID=TIR,Number=2,Type=Integer,Description="Reads strongly supporting indel allele for tiers 1,2">

I want to calculate VAF, so I am confused by the difference of alternate allele versus indel allele ; Which one I should use for calculating Variant Allele Frequency (VAF)?

Answer 1

[ATpoint]

The manual contains a section on how to calculate AFs: https://github.com/Illumina/strelka/tree/master/docs/userGuide#somatic

For somatic indels:

tier1RefCounts = First comma-delimited value from FORMAT/TAR
tier1AltCounts = First comma-delimited value from FORMAT/TIR
Somatic allele freqeuncy is $tier1AltCounts / ($tier1AltCounts + $tier1RefCounts)

Alternate vs. indel allele question answered by the lead developer, see https://groups.google.com/forum/#!topic/strelka-discuss/Pz9EYKnE6u8 (found via a commonly used search engine).

[zizigolu]

Thank you I read all you kindly posted but still not quite sure should I use Alternate or indel allele in this formula?

Somatic allele freqeuncy is $tier1AltCounts / ($tier1AltCounts + $tier1RefCounts)