BCFtools for somatic vs. germline variant calling

BCFtools for somatic vs. germline variant calling

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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!


RNA-seq


germline


calling


bcftools


variant

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