check duplicates in two columns
Hi all!
I have two different files: a .map (from illumina genotyping with bead chip) and a .vcf (from NGS of a Pools of individuals). I'm interested in finding variations that are in both files, so I would have to compare for column 1: #CHROM and 4: POS (for .map) and column 1 #CHROM and 2: POS (for .vcf) to obtain some variations that are in common. I tried using awk but without success. Any suggestions will be very appreciated.
Greetings
Marco
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Can you post your awk command?
On stackoverflow.com you will find "thousands" of questions related to this issue.
On biostars too :-)
check if two columns match in 2 annotation files and print those lines to a new output file
Yup, that's true, but not thousands :-P.
You win. Technically.
Thank you for the answers, my awk command is:
where
$1and$2are#CHROMandPOSin the .vcf file and$1and$4are#CHROMandPOSfor the .map file