Question: Getting information of individual sample from merged sample
0
gravatar for hafiz.talhamalik
3 months ago by
Pakistan
hafiz.talhamalik230 wrote:

I have a merged vcf file, last 8 columns are about the information of my 8 sample weather variant was there in the respective sample or not ?

3   196139511   .   C   A   122 PASS    VDB=0.101032;RPB=-1.22822;AF1=0.5;AC1=1;MQ=60;FQ=125;PV4=1,1,1,1;DP=13;DP4=3,4,3,3;AN=2;AC=1    GT:PL:GQ    ./.:.:. ./.:.:. ./.:.:. ./.:.:. ./.:.:. 0/1:152,0,175:99    ./.:.:. ./.:.:.
3   196144312   .   C   T   137 PASS    VDB=0.104742;AF1=1;AC1=2;MQ=60;FQ=-45;DP=10;DP4=0,0,4,2;AN=2;AC=2   GT:PL:GQ    ./.:.:. 1/1:170,18,0:33 ./.:.:. ./.:.:. ./.:.:. ./.:.:. ./.:.:. ./.:.:.
3   196144517   .   C   A   101 PASS    VDB=0.078549;RPB=0.317149;AF1=0.5;AC1=1;MQ=60;FQ=104;PV4=0.57,1,1,1;DP=11;DP4=4,2,2,3;AN=2;AC=1 GT:PL:GQ    ./.:.:. ./.:.:. ./.:.:. 0/1:131,0,152:99    ./.:.:. ./.:.:. ./.:.:. ./.:.:.

my question is how can I get to know that if a sample doesnt contain a respective variant than weather there was same allele as reference or there was no read matched at that position ? keeping in mind I have few thousand snps and I cant check each of them indivisualy using IGV or tablet viewer.

sequencing alignment vcf • 100 views
ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 3 months ago by hafiz.talhamalik230
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1744 users visited in the last hour