compare two ped files with different number of snp information
Hi,
I have two ped(file1.ped-2364 subjects, file2.ped-2345 subjects) files from the sequencing centre sequenced for 12snps(file1.map), 3snps(file2.map) separately. The ped files have genotype information for different number of subjects. I would like to compare both ped files and know which subjects have missing information. Could you please advise on the approach ?
Thanks.
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See plink's --merge option.
I have used the --merge option for combining the two ped files and got information for 2397 subjects. I would like to which subjects do not have information in first ped file and in second ped file. I couldn't find the --merge-mode option giving this information. Are you referring to any other option ? Thanks !