Comments (1)
chrisamiller
commented on August 28, 2024
If you have VCF files, you may or may not already have what you need. For somatic calling, these are often stored in Allelic Depth(AD) and Allelic Fraction (AF) fields in the VCF. If not, you can use bam-readcount to add this information. One example of how to do this is here: https://pvactools.readthedocs.io/en/latest/pvacseq/input_file_prep/readcounts.html Copy number can be called by many different algorithms - CNVkit is one that we've had good luck with in the past. Best of luck
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