Problem merging plink files for somatic variants.

Question

[Palgrave]

I have 5000 somatic vcf files converted to plink format that I try to merge using this command

plink --bfile file1 --merge-list files.bed.txt --make-bed --out Merged.Plink

However, the output looks strange and I get several errors (1107578 to be exact) like below: Any ideas?

...
Warning: Multiple chromosomes seen for variant 'gridss335fb_1314h'.
Warning: Multiple chromosomes seen for variant 'unbalanced_22'.
Warning: Multiple chromosomes seen for variant 'gridss1070bb_15h'.
Warning: Multiple chromosomes seen for variant 'gridss584ff_92h'.
Error: 797428 variants with 3+ alleles present.
* If you believe this is due to strand inconsistency, try --flip with
  Merged.Plink-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.

End time: Sat Mar  9 08:19:15 2024

The output:

head Merged.Plink-merge.fam
ACTN01020001R   ACTN01020001R   0   0   0   -9
ACTN01020001T   ACTN01020001T   0   0   0   -9
ACTN01020002R   ACTN01020002R   0   0   0   -9
ACTN01020002T   ACTN01020002T   0   0   0   -9
ACTN01020003R   ACTN01020003R   0   0   0   -9
ACTN01020003T   ACTN01020003T   0   0   0   -9
ACTN01020005R   ACTN01020005R   0   0   0   -9
ACTN01020005T   ACTN01020005T   0   0   0   -9
ACTN01020006R   ACTN01020006R   0   0   0   -9
ACTN01020006T   ACTN01020006T   0   0   0   -9


 wc Merged.Plink-merge.missnp
  797428   797428 12522503 Merged.Plink-merge.missnp

[Pierre Lindenbaum]

Don't forget to follow up on your threads, that is bad etiquette. If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one answer if they all work. If an answer was not really helpful or did not work, provide detailed feedback so others know not to use that answer.

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[Palgrave]

Sorry, finxed now.