I tried to merge plink files for c21 and c22 with plink (bed, bim, fam) and I have this error:
Error: 1 variant with 3+ alleles present.
* If you believe this is due to strand inconsistency, try --flip with
WGS_200k_ukb24305_c21-22_b0_v1-merge.missnp.
(Warning: if this seems to work, strand errors involving SNPs with A/T or C/G
alleles probably remain in your data. If LD between nearby SNPs is high,
--flip-scan should detect them.)
* If you are dealing with genuine multiallelic variants, we recommend exporting
that subset of the data to VCF (via e.g. '--recode vcf'), merging with
another tool/script, and then importing the result; PLINK is not yet suited
to handling them.
See https://www.cog-genomics.org/plink/1.9/data#merge3 for more discussion.
Do you have any suggestion?
Thanks a lot,
Best
If you are merging files that are missing some allele codes?e.g. single-sample files that were imported from .ped or 23andMe format, or multi-sample files imported from .ped and never filtered on MAF?and they were processed by PLINK 2.0 before merging, you may need to update your PLINK 1.9 build. PLINK 1.9 builds before Jan 2023 did not explicitly recognize the missing allele code emitted by PLINK 2.0; this was usually harmless, but broke merge.
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What is the date of your plink 1.9 version?
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