Question: merging plink files
1
gravatar for stalo_92
2.2 years ago by
stalo_9210
stalo_9210 wrote:

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

mergefiles plink • 1.2k views
ADD COMMENTlink written 2.2 years ago by stalo_9210
1
gravatar for christopher medway
2.2 years ago by
Cardiff, UK
christopher medway440 wrote:

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?

ADD COMMENTlink modified 2.2 years ago • written 2.2 years ago by christopher medway440

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

ADD REPLYlink written 2.2 years ago by stalo_9210
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