Best variant caller for CNVkit

Question

[milos-91]

Hi! What variant caller has proven to give the best results with CNVkit?

Answer 1

[Eric T.]

For SNVs, any variant caller that will do joint genotyping of the tumor and normal samples without dropping germline variants is fine. VarDict is good, and FreeBayes is fine too. Mutect2 unfortunately drops the germline variants, which CNVkit needs for LOH detection. See here: https://cnvkit.readthedocs.io/en/stable/fileformats.html#vcfformat

You can also use HaplotypeCaller or Samtools to force-call the tumor sample with a list of known SNP sites, in case you don't have a matched normal or if your pipeline only runs Mutect2.