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?