I really try to find some clear answer on Google, but it seems to me, that VarScan parameters understand only their creators.
I would prefer if somebody explain me (on example) what is doing parameter min-Reads2 in VarScan Germline caller.
I tried to change on set of Samples this value to:
min-reads2=1 ----> number of SNPs = 58 min-reads2=2 ----> number of SNPs = 58 min-reads2=3 ----> number of SNPs = 58 min-reads2=4 ----> number of SNPs = 58 min-reads2=20 ---->number of SNPs = 31
So only different was when I set up min-Reads2 to high value. When I compare all vcf - I can see, that missing 27 variants are only where AC=1 appears (Allele count in genotypes). So probably filter min-Reads2 depend on AC value.
Does anybody understand this parameter. Please do not copy explanation from manual (Minimum supporting reads at a position to call variants ) I need explanation on example.
Thank you very much.