could anyone explain why the --cosmic option is removed?
Also, should --germline_resource be used with --dbsnp
or replace it?
I think the germline resource and PoN replace the cosmic input.
Inputting the dbsnp file does nothing other than populate the rsid field. It is up to you to determine whether you are interested in those. The germline resource helps to filter out possible germline variants, so you should input that any time you run Mutect2.
P.S. You may find the Mutect2 tutorial helpful as well.
Thanks @Sheila ! May I ask a couple of questions:
1. In the best practice for Mutect1 Somatic variant calling , the dbsnp is redlist, is it only used for RSid as well?
2. why not keeping cosmic as a whitelist in Mutect2?
1) No, I think in Mutect1, dbSNP was used as a "blacklist" file. The sites in it would be considered germline risk.
2) I think the team found in testing that using a germline resource, PoN, and matched normal is enough to filter out possible germline variants. The variants in the tumor sample that pass the thresholds are most likely somatic mutations, so there is no need for a "whitelist".
I hope that helps.
What is a germline resource when using a non-model organism? Is it the same as the truthset that is created of known sites?
Germline resource , such as gnomAD, contains population allele frequencies of common and rare variants and used for somatic variant calling.