Hello everyone,

I am trying to use Varscan to find somatic variants but I want to apply filters on the minimum variant frequency and minimum number of variant reads. I have tumor-normal paired samples.

In this case, should I use:
a) mpileup2snp and mpileup2indel separately and indicate the filters
or
b) somatic and then somaticFilter on each one of the files produced (snps and indels)?

Is there a difference in how these two approaches work?
Also, I want the output in vcf format and according to the manual, only mpileup2snp/mpileup2indel offes that option?

Thanks!
It is the second workflow that you want. I have [a script][1] in my Github that uses VarScan2 for somatic calling (not saying it is a nice one or fulfills any good-practice standard when it comes to style or whatever), but you might get some inspiration from it. It also uses `GNU parallel` to parallelize the process over all chromosomes.

It starts by calling the raw variants with `VarScan2 somatic`, then separates them into somatic and germline with `processSomatic`, selects high-confidence variants with on `VarScan`'s Fisher's Exact Test, and finally runs the heuristic `fpfilter` to remove junk calls.


  [1]: https://github.com/ATpoint/Variant_Calling/blob/master/VarScan2/VarScan2_Somatic.sh