Question: Getting information of individual sample from merged sample
0
gravatar for hafiz.talhamalik
14 months ago by
Pakistan
hafiz.talhamalik290 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 • 246 views
ADD COMMENTlink modified 14 months ago by Biostar ♦♦ 20 • written 14 months ago by hafiz.talhamalik290
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: 1165 users visited in the last hour
_