BCFtools for somatic vs. germline variant calling

Question

[rebeliscu]

Hi there,

I have seen the workflow 'mpileup > call' using BCFtools discussed in the context of both germline and somatic variant calling.

It's not clear to me, then, how the program differentiates between the two. If I'm seeking to identify strictly germline variants, can I take the output of this workflow as is? Or do I need to somehow filter out variants that might be considered somatic?

Hope my questions make sense.

Thanks!

Answer 1

[Ram]

bcftools does not differentiate. It calls variant loci. I don't think there's a single variant caller that calls both germline and somatic calls, as they're fundamentally different.

A germline variant is a difference between an individual's germline DNA and the reference genome.

A somatic variant is a difference between an individual's tumor sequence, their matched normal sequence, and the reference sequence. (..., somatic variants are both (i) different from the control sample and (ii) different from the reference. What this means is that if a site is variant in the control but in the somatic sample reverts to the reference allele, then it is not a somatic variant.)

See: https://gatk.broadinstitute.org/hc/en-us/articles/360035890491