Variant Call File Completion Varification

[arcolombo698]

Hello.

I am just inquiring if whether the VCF conversion processed completely. in my job report it said :


[bcfview] 100000 sites processed.
[afs] 0:92071.007 1:4605.800 2:3323.192
[afs] 0:75428.076 1:4325.300 2:3606.623
[afs] 0:40896.181 1:2507.646 2:1959.174
[afs] 0:32411.039 1:1569.609 2:1122.352
[afs] 0:28658.411 1:1206.773 2:846.816
[afs] 0:30663.994 1:2180.141 2:1601.864
[afs] 0:49943.377 1:3061.805 2:2377.817
[afs] 0:35460.294 1:2423.947 2:1893.759


Now In other jobs the processes are up to 200000 sites processed. My VCF files are a little smaller than normal and I just want a way to check if I have the entire vcf file processed completely.

I looked at the "tail Sample.vcf" and it output


chrY 21154569 . A G 222 . DP=63;VDB=0.0271;AF1=1;AC1=2;DP4=0,0,25,37;MQ=50;FQ=-214 GT:PLP:SP:GQ 1/1:255,187,0:62:0:99
chrY 21154603 . A C 222 . DP=37;VDB=0.0347;AF1=1;AC1=2;DP4=0,0,13,22;MQ=50;FQ=-132 GT:PLP:SP:GQ 1/1:255,105,0:35:0:99


and this means that I have sites ranging up to 21154603.

Not sure how to check the information i processed.

thank you

AC

[arcolombo698]

My reads are around 17-20 million reads and I am not sure how this relates to the report that 100,000 sites were processed.