To Identify Variants
I have a .vcf file which I generated by using bcftools. After I ran .bcftools I used vcfutils.pl varfilter to filter the variants. The output vcf file consist of:
I am writing here the first line after the header ##
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT SAMPLE1 SAMPLE2 SAMPLE3 SAMPLE4 SAMPLE5 SAMPLE6 SAMPLE7 SAMPLE8 SAMPLE9 SAMPLE10 SAMPLE11
Reference 2981 . T A 126 . DP=249;VDB=0.600819;SGB=9.65108;RPB=0.997745;MQB=1;BQB=0.768244;MQ0F=0;AC=1;AN=11;DP4=235,0,11,0;MQ=60 GT:PL 0:0,196 1:165,0 0:0
I found a similar post Best way to compare two samples in a VCF file but it includes two different vcf files. I just have one vcf and I need to identify variants from 11 different samples. I am trying to extract only those mutations found in SAMPLE2 SAMPLE3 and SAMPLE4 SAMPLE5 SAMPLE6 SAMPLE7 SAMPLE8 SAMPLE9 SAMPLE10 SAMPLE11
It would be a great help if anyone of you help me to figure out the step.
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