Dear All,

For three samples, I generated vcf files using samtools, gatk, and varscan.

I tried accessing the files 1000G_phase1_high_confidence_snps.vcf, it has only following columns 1) Chrom, 2) Pos, 3) ID, 4) Ref, 5) Alt, 6) Qual, 7) Filter and 8) Info.

I have vcf files with following columns samtools: 1) Chrom, 2) Pos, 3) ID, 4) Ref, 5) Alt, 6) Qual, 7) Filter, 8) Info and 9) Sample1. varscan: 1) Chrom, 2) Pos, 3) ID, 4) Ref, 5) Alt, 6) Qual, 7) Filter, 8) Info and 9) Sample1. gatk:1) Chrom, 2) Pos, 3) ID, 4) Ref, 5) Alt, 6) Qual, 7) Filter, 8) Info and 9) Sample1.

Now I want to compare those vcf files generated by samtools, gatk and varscan against with 1000G_phase1_high_confidence_snps.vcf to find out which variant caller gives the same list of high confident mutations from 100G_phase1?