convert and merge somatic vcf file to plink format

Question

[Palgrave]

I want to convert vcf files to plink format, but the vcf are missing IDs (annotated as "." for all variants) instead of the usual rsXXX that we usually see for germline mutations. After I convert I try to merge all the plink files using this command:

plink --bfile sample1.vcf --merge-list files.bed.txt --make-bed --out Merged.Plink

But I get a lot of warnings:

Warning: Multiple chromosomes seen for variant '.'.

Is it possible to work with somatic vcf files using plink?

Answer 1

[LChart]

You can use --set-missing-var-ids "@:#" to re-set the (missing) variant IDs to chromosome:position nomenclature. See https://www.cog-genomics.org/plink/1.9/data#set_missing_var_ids.