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Mutect1 call stats and ACNV seg analogues in GATK4 for deTiN input?
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 188.8.131.52? For example, do
tau referred to here https://github.com/broadinstitute/deTiN/wiki/Description-of-inputs relate to
LOG2_COPY_RATIO_POSTERIOR_50 respectively in GATK4 ModelSegments output?