Question: Mpileup By Samtools And How To Get The Counts Per Allele Per Position In The Vcf
gravatar for Deniz
9.4 years ago by
Deniz210 wrote:


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


I really appreciate any help.

vcf mpileup snp • 4.0k views
ADD COMMENTlink modified 9.4 years ago by Pierre Lindenbaum134k • written 9.4 years ago by Deniz210

waiting for your thoughts..

ADD REPLYlink written 9.4 years ago by Deniz210

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

ADD REPLYlink written 9.0 years ago by Juliofdiaz130
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