merging plink files

Question

[stalo_92]

i have been trying to merge some ped/map files. i had removed or renamed the duplicated in the map file so i no longer get a duplication warning.

/home/chrystalla/plink-1.07-x86_64/plink --bfile snp_exc_1 --merge snp_exc_2.map snp_exc_2.ped --make-bed --out lets_merge

ERROR: Problem with MAP file line: F102 PN12-4100 0 0 1 2 T T G A C C 0 0 C C 0 0 T C A A A T C C C C C C A G C C A A C C A A 0 0 A A G G G G A T C T T C G G C C C A T T A A G T G G A G C T C C A C A A A G G G A G G G A A T T T T C C T T T T G A T T A A A A C C T T G A G G A A T T G G 0 0

i try merging them after converting them into the binary format (bed etc) but the process is just killed

Analysis started........... Reading genotype bitfile from [ more_exc_1.bed ] Detected that binary PED file is v1.00 SNP-major mode Using merge mode 1 : consensus call (default) Killed

can you help me?

thanks

Answer 1

[christopher medway]

The MAP line generated in the error looks like a PED line. Either your files (.map .ped) are named incorrectly, or you need to change the order you read them into PLINK.

Your FID and IID should be alphanumeric. Removing the '-' may help?

[stalo_92]

thank you very much, changing the order of the files was enough. :)