Error in Plink2 --alt-allele

[kaustubh...@gmail.com]

Hi Chris,

When I run --a1-allele with Plink 1.9 on my data, it works fine, but when I use it (or the equivalent --alt-allele) in Plink 2 it gives me the following error:

 

Error: Duplicate allele code in variant '22:24301858_CNV_GSTT2B_Ilmndup1' at position 0:0.

It is true that I have several variants with chr 0 and bp 0, as is common with unfiltered data exported from Illumina chips, but Plink 1.9 works fine with it. Below is my equivalent sets of code for Plink 1.9 and Plink 2, and I also attach the log files. The error is in test.plink2.log.

plink2 --pfile Chandana_KA3 --update-ids remove_fid.txt --flip strand_flip.txt --make-bed --out input.plink1
plink --bfile input.plink1 --a1-allele SNP_Table_alleles.txt 3 1 --make-bed --out test.plink1

plink2 --pfile Chandana_KA3 --update-ids remove_fid.txt --flip strand_flip.txt --make-pgen --out input.plink2
plink2 --pfile input.plink2 --alt-allele SNP_Table_alleles.txt 3 1 --make-pgen --out test.plink2

Thanks,

Kaustubh.

[Chris Chang]

The issue is the duplicate allele code (REF and ALT are identical for that variant), not the 0:0 position.  That's invalid input, and you should either correct or remove that variant (plink2 does still let you --exclude it by ID) before running --a1-allele/--alt-allele.

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