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Old 12-23-2015, 11:27 PM   #1
kumar03
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Location: India

Join Date: Dec 2015
Posts: 4
Default Nucleotide variation from multi-sample vcf file

Dear all,

I have an SNP information's from single vcf file consists of muti-samples (44 individuals). In order to get the nucleotide variations of my samples was separated into 44 vcf files using vcf-subset. Then i have checked SNP information and noticed that each sample has same nucleotide bases with corresponding position. Could anybody let me know how to handle this?
Is there any alternate way to get those variations from multi-sampled VCF file?

Multi-sample vcf file

##fileformat=VCFv4.1
##
.
.
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1.bam S2.bam S3.bam . . . etc
A10 78849 . G A . PASS AR2=0.922;DR2=0.945;AF=0.763 GT:DS:GP 0|0:0:1,0,0 0|0:0:1,0,0 0|0:0:1,0,0 1| ... etc
.
Etc,.


After separation (1st sample)

##fileformat=VCFv4.1
##
.
.
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT S1.bam
A10 78849 . G A 999 . DP=9196;AC=0;AN=2 GT:PL:DP:GQ 0/0:0,232,65:77:55
.
Etc,.
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