Mpileup By Samtools And How To Get The Counts Per Allele Per Position In The Vcf

Question

[Deniz]

Hello,

I have 6 different samples and looking for allele specific SNPs. I aligned 36bp to human genome and then used samtools mpileup option to get vcf files.

I got one vcf file for each sample which compares hg18 and sorted bam file and saved it as sample1.vcf

then I put all six together to get one combined big vcf files.

then I took all dp4 values for each sample and insert them into big combined file.

So how can I get how many are Cs, As, Ts and Gs? how to get the counts per allele per position in the vcf

this is one exmple: I put/insert dp4 values for sample 1 into main file.I dont know how to get the counts per allele per position in the vcf

chr1    948692    .    G    A    999    .    DP=94;AF1=0.7087;CI95=0.625,0.7917;DP4=1,22,4,50;MQ=20;FQ=999;PV4=1,5.6e-43,1,0.48    GT:PL:GQ:**DP4**    1/1:49,9,0:10:**0,0,0,4**    1/1:20,3,0:5    0/0:0,24,83:17    0/0:0,18,91:12
chr1    951628    .    A    T    999    .    DP=32;AF1=0.9972;CI95=0.75,1;DP4=0,1,18,11;MQ=20;FQ=-27.4;PV4=0.4,3.8e-11,1,1    GT:PL:GQ:**DP4**    0/1:44,0,8:3:**0,1,2,1**    1/1:0,0,0:8    1/1:88,24,0:32    1/1:51,12,0:20
chr1    1311078    .    G    T    999    .    DP=66;AF1=0.5645;G3=0.363,0.01773,0.6193;HWE=0.0107;CI95=0.4167,0.6667;DP4=12,21,5,28;MQ=20;FQ=999;PV4=0.09,4.6e-42,1,0.18    GT:PL:GQ:**DP4**    1/1:57,9,0:8:**0,0,1,1**    1/1:20,3,0:3    0/0:0,21,79:17    0/0:0,39,160:35
chr1    2222583    .    T    C    999    .    DP=31;AF1=1;CI95=0.9167,1;DP4=0,0,0,30;MQ=20;FQ=-35.1    GT:PL:GQ:**DP4**    1/1:36,6,0:21:**0,0,0,2**    1/1:20,3,0:18    1/1:35,6,0:21    1/1:67,15,0:30
chr1    2526746    .    A    G    34.4    .    DP=5;AF1=0.7814;CI95=0.25,0.9583;DP4=1,0,4,0;MQ=20;FQ=-15.2;PV4=1,0.022,1,1    GT:PL:GQ:DP4    1/1:36,6,0:7:0,0,2,0    0/1:0,0,0:3    0/1:0,0,0:3    1/1:20,3,0:5
chr1    3780339    .    C    T    3.17    .    DP=7;AF1=0.2095;CI95=0.04167,0.4583;DP4=1,4,1,1;MQ=20;FQ=3.72;PV4=1,0.0016,1,1    GT:PL:GQ:DP4    0/1:40,6,0:8:0,0,1,1    0/0:0,0,0:8    0/0:0,3,20:10    0/0:0,0,0:8
chr1    4078371    .    T    C    4.54    .    DP=34;AF1=0.223;CI95=0.04167,0.4167;DP4=3,21,0,4;MQ=20;FQ=5.25;PV4=1,2.8e-09,1,1    GT:PL:GQ:DP4    0/1:36,6,0:6:0,0,0,2    0/1:14,0,14:9    0/0:0,0,0:6    0/0:0,3,20:9

Thanks

I really appreciate any help.

[Deniz]

waiting for your thoughts..

[Juliofdiaz]

Did you ever solve this problem? Also you can probably tag this topic with "samtools"