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Mutect1 call stats and ACNV seg analogues in GATK4 for deTiN input?

sraosrao OxfordMember

Hi, I would like to generate a call-stats for deTiN (https://github.com/broadinstitute/deTiN/wiki/How-to-generate-inputs-using-GATK) to account for tumour in normal contamination. Is this possible only in Mutect 1 or is there an equivalent in GATK4 Mutect2 too?

Similarly, is there an equivalent way to generate the SNP statistics file and aSCNV seg file using GATK 4.0.6.0? For example, do f and tau referred to here https://github.com/broadinstitute/deTiN/wiki/Description-of-inputs relate to MINOR_ALLELE_FRACTION_POSTERIOR_50 and LOG2_COPY_RATIO_POSTERIOR_50 respectively in GATK4 ModelSegments output?

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