check duplicates in two columns

Question

[marcoabbestia]

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

[iraun]

On stackoverflow.com you will find "thousands" of questions related to this issue.

[PoGibas]

On biostars too :-)

check if two columns match in 2 annotation files and print those lines to a new output file

[iraun]

Yup, that's true, but not thousands :-P.

[Ram]

You win. Technically.

[PoGibas]

Can you post your awk command?

[marcoabbestia]

Thank you for the answers, my awk command is:

awk -F'\t' 'NR==FNR{c[$1$2]++;next};c[$1$4] > 0' file.vcf file.map

where $1 and $2 are #CHROM and POS in the .vcf file and $1 and $4 are #CHROM and POS for the .map file