I am currently using samtools/bcftools to call SNPs. My question is, how does samtools/bcftools call out alternative alleleS as opposed to the reference?
ctg1117585322335 54283 . A G,T 49 . DP=21;AF1=1;CI95=1,1;DP4=0,0,0,21;MQ=29;FQ=-87 GT:PL:GQ 1/1:82,60,0,82,47,79:99
mpileup ctg1117585322335 54283 A 21 ggggggggggggggggtgggg 333333344343343304444
ctg1117585322225 4142 . C T,G 185 . DP=29;AF1=1;CI95=1,1;DP4=0,0,0,29;MQ=53;FQ=-108 GT:PL:GQ 1/1:218,81,0,209,47,203:99
mpileup ctg1117585322225 4142 C 29 ttttttttttttttgttttttttttttgt JIIJJIIJJIJIJI9JJFI:IIIHJIJ2C
From example 1, the reported depth is 21. As shown in mpileup, G has a depth of 20 as opposed to T which has 1. In this case, I would like to further filter the SNPs found where only the SNPs that has more than a depth of 10 would be called.
When calling for alternative alleleS, is there a cut-off in terms base quality/depth for the second alternative allele ( in this case, T) to be called?