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Test-drive the GATK tools and Best Practices pipelines on Terra
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We will be out of the office on November 11th and 13th 2019, due to the U.S. holiday(Veteran's day) and due to a team event(Nov 13th). We will return to monitoring the GATK forum on November 12th and 14th respectively. Thank you for your patience.
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 126.96.36.199? 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?