Fixed handling of allele depths for Indels called by Strelka (#215)
Fixed handling of allele depths for Indels called by Strelka (#215)

Fixed handling of alternate and reference allele depths. Currently, only the variant allele depth (from TIR) is translated to MAF. However, the information for the reference allele is similarly located in TAR, which is now extracted as well.  

Compare Strelka's updated README: https://github.com/Illumina/strelka/blob/master/docs/userGuide/README.md#somatic 

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)
ckandoth/vcf2maf