Hi GATK team,
Our lab has been in the process of exploring CNV calling methods for WGS. We've found that GATK4's somatic CNV calling pipeline (following the tutorial outlined here) does a great job with segmentation after some adjustments. This is the pipeline we are currently using: https://portal.firecloud.org/?return=terra#methods/gatk/CNV_Somatic_Pair_Workflow/7. We're using the latest version of GATK (126.96.36.199)
I have a few questions related to the outputs of this workflow. In particular, we'd like to get outputs that can be ingested by ABSOLUTE and by DeTiN. These were previously generated by AllelicCNV or AllelicCapseg.
Previously, GATK's AllelicCNV tool generated an ACS-like file (-sim-final.acs.seg), which contained allelic copy ratio data and could be used by ABSOLUTE and DeTiN. Judging by this GitHub discussion, ModelSegments is supposed to replace AllelicCNV, but it does not produce a file like *-sim-final.acs.seg - only a file that contains total copy ratio and minor allele frequencies.
What is the best way to generate an allelic segmentation file that can be used for ABSOLUTE and DeTiN? I had planned to simply run the older version of AllelicCNV (or AllelicCapseg), but A) I don't want to use old tools if something new is available, and B) I'm not sure where to get the inputs for these tools using the updated workflow. In particular, AllelicCNV and AllelicCapseg require the tangent-normalized read counts (previously output by NormalizeSomaticReadCount as the .tn.tsv file). Is the corresponding output in the new workflow the .denoisedCT.tsv file generated by DenoiseReadCounts? The other two inputs (the tumor het results and the seg file) presumably come from ModelSegments (.hets.tsv and .modelFinal.seg)
Thanks for any help!
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