Question: Mpileup And Snp Calling
1
gravatar for User 7317
7.6 years ago by
User 731710
User 731710 wrote:

I am reading the mathematical on Samtools Algorithms to understand how mpileup works. I ran mpileup per each sample and multiples samples.

/share/bin/samtools-0.1.16/samtools mpileup -Euf 0.1.16/bcftools/vcfutils.pl varFilter -D100 > 1_Euf.flt.vcf

and I also run 1.sorted.bam 2.sorted.bam together.

I compared 1Euf.flt.vcf, 2Euf.flt.vcf, 1and2_Euf.flt.vcf with venn diagram. Looked for overlap and unique regions.

10176 SNPs 1_Euf.flt.vcf
10649 SNPs 2_Euf.flt.vcf
18000 SNPs 1and2_Euf.flt.vcf

3102 SNPS overlap of three files without header lines

1728 unique_1_Euf.flt.vcf
181 unique_2_Euf.flt.vcf
2227 unique_3_Euf.flt.vcf

unique1Euf.flt.vcf This is only unique to 1st file and didnt show up in vcf files of together files. I dont understand why. When I call variants from multiple sorted bams with mpileup, I dont see these 1728 positions. I really want to understand main reasons and algorthms. Could you explain basicly the how mpileup works on multiple files and single files.

When I look into together.vcf file, There are 2227 SNP positions didnt show up in each separete vcf files. this can be due to the sum of read count of each files exceed the threshold and show up in together file, right? Is there any other explanations?

chr16   27250658        .       A       T       6.02    .       DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=20;FQ=-33;SF=0     GT:PL:GQ        1/1:36,6,0:6

chr16   27367972        .       G       A       6.02    .       DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20;FQ=-33;SF=0     GT:PL:GQ        1/1:36,6,0:6

chr16   27561584        .       G       A       24      .       DP=4;AF1=1;CI95=0.5,1;DP4=0,0,2,1;MQ=20;FQ=-36;SF=0     GT:PL:GQ        1/1:56,9,0:15

chr16   27729524        .       C       T       26      .       DP=10;AF1=0.5002;CI95=0.5,0.5;DP4=1,2,5,1;MQ=20;FQ=6.19;PV4=0.23,0.3,1,1;SF=0   GT:PL:GQ        0/1:56,0,32:35

chr16   28890941        .       T       G       6.02    .       DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20;FQ=-33;SF=0     GT:PL:GQ        1/1:36,6,0:6

chr16   28937275        .       G       A       3.64    .       DP=3;AF1=0.5205;CI95=0.5,0.5;DP4=0,1,1,1;MQ=20;FQ=-16.1;PV4=1,1,1,1;SF=0        GT:PL:GQ        0/1:31,0,11:18

chr16   29777088        .       C       A       9.31    .       DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=20;FQ=-33;SF=0     GT:PL:GQ        1/1:40,6,0:8

chr16   29808708        .       C       G       6.02    .       DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=20;FQ=-33;SF=0     GT:PL:GQ        1/1:36,6,0:6

chr16   29822841        .       A       C       9.31    .       DP=2;AF1=1;CI95=0.5,1;DP4=0,0,1,1;MQ=20;FQ=-33;SF=0     GT:PL:GQ        1/1:40,6,0:8

chr16   30102802        .       T       C       6.02    .       DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20;FQ=-33;SF=0     GT:PL:GQ        1/1:36,6,0:6

chr16   30457350        .       C       T       37.5    .       DP=4;AF1=1;CI95=0.5,1;DP4=0,0,1,3;MQ=20;FQ=-39;SF=0     GT:PL:GQ        1/1:70,12,0:21

chr16   30759716        .       T       C       17.1    .       DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=20;FQ=-36;SF=0     GT:PL:GQ        1/1:49,9,0:15

chr16   30926303        .       G       C       6.02    .       DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=20;FQ=-33;SF=0     GT:PL:GQ        1/1:36,6,0:6

chr16   30960507        .       T       C       6.02    .       DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20;FQ=-33;SF=0     GT:PL:GQ        1/1:36,6,0:6

chr16   31044683        .       A       G       26      .       DP=6;AF1=0.5032;CI95=0.5,0.5;DP4=0,2,2,2;MQ=20;FQ=-8.63;PV4=0.47,0.16,1,0.2;SF=0        GT:PL:GQ        0/1:56,0,19
:22

chr16   31085470        .       T       C       6.02    .       DP=4;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=20;FQ=-33;SF=0     GT:PL:GQ        1/1:36,6,0:6

chr16   33503129        .       C       T       6.02    .       DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=20;FQ=-33;SF=0     GT:PL:GQ        1/1:36,6,0:6

chr16   33866630        .       G       T       6.02    .       DP=2;AF1=1;CI95=0.5,1;DP4=0,0,0,2;MQ=20;FQ=-33;SF=0     GT:PL:GQ        1/1:36,6,0:6

chr16   33894371        .       A       G       15.1    .       DP=4;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=20;FQ=-36;SF=0     GT:PL:GQ        1/1:47,9,0:14

chr16   33894379        .       A       T       8.93    .       DP=4;AF1=0.543;CI95=0.5,1;DP4=1,0,3,0;MQ=20;FQ=-19;PV4=1,0.0068,1,1;SF=0        GT:PL:GQ        0/1:38,0,8:12

chr16   33897385        .       T       C       6.02    .       DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20;FQ=-33;SF=0     GT:PL:GQ        1/1:36,6,0:6

chr16   33901775        .       A       G,C     3.41    .       DP=3;AF1=1;CI95=0.5,1;DP4=0,0,0,3;MQ=20;FQ=-33;SF=0     GT:PL:GQ        1/1:43,17,11,31,0,28:4

chr16   33922739        .       A       G       17.1    .       DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=20;FQ=-36;SF=0     GT:PL:GQ        1/1:49,9,0:15

chr16   33922743        .       A       C       17.1    .       DP=3;AF1=1;CI95=0.5,1;DP4=0,0,3,0;MQ=20;FQ=-36;SF=0     GT:PL:GQ        1/1:49,9,0:15

chr16   33946169        .       C       T       6.02    .       DP=2;AF1=1;CI95=0.5,1;DP4=0,0,2,0;MQ=20;FQ=-33;SF=0     GT:PL:GQ        1/1:36,6,0:6

chr16   33950474        .       A       G       80.1    .       DP=14;AF1=1;CI95=0.5,1;DP4=2,0,7,4;MQ=20;FQ=-28;PV4=1,0.3,1,0.17;SF=0   GT:PL:GQ        1/1:
bcftools samtools mpileup snp • 2.8k views
ADD COMMENTlink modified 7.6 years ago by brentp23k • written 7.6 years ago by User 731710
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