Merging multiple .ped/.map files for PLINK analisys purposes

Question

[giusdalt95]

Good moring everyone! I am trying to merge 5 couple of flat-format .ped/.map files with PLINK command:

plink --noweb --file 53519559 --merge-list allfiles.txt --recode --out merged

but the terminal gives me back this error:

Found 54 SNPs that do not match in terms of allele codes
Might include strand flips, although flipped A/T and C/G SNPs will be undetected)
Writing problem SNPs to [ merged.missnp ]

ERROR: Stopping due to mis-matching SNPs -- check +/- strand?
  

N.B: I am due to specify that I started from 5 VCF files, from which I filtered for SNPs, removed duplicate positions and filtered out SNPs with missing rsID; subsequently I used vcftools to convert the filtered vcf files in plink format, through the code:

vcftools --gzvcf my.vcf.gz --plink --out myfileconverted

If someone could help me I would be very grateful! P.S: obviously don't hesitate to ask if you need more infos about.

Answer 1

[chrchang523]

See the discussion of merge failures at https://www.cog-genomics.org/plink/1.9/data#merge3 .