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chrchang / plink-ng

A comprehensive update to the PLINK association analysis toolset. Beta testing of the first new version (1.90), focused on speed and memory efficiency improvements, is finishing up. Development is now focused on building out support for multiallelic, phased, and dosage data in PLINK 2.0.

Home Page:https://www.cog-genomics.org/plink/2.0/

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Error: REF allele on line 1071 of --pgen-diff .pvar file conflicts with loaded REF allele

hsmith9002 opened this issue · comments

commented

Hi,

This is the full error message.

"Error: REF allele on line 1071 of --pgen-diff .pvar file conflicts with loaded
REF allele, and neither are flagged as provisional."

Can you help me understand what is going wrong here. I wasn't able to find this error in your documentation. Here are the lines leading up to the error:

./plink2 --vcf ${GTAK}.vcf.gz --double-id --make-pgen --sort-vars --out ${GTAK}

./plink2 --vcf ${DNANEXUS}_chr22.vcf.gz --double-id --make-pgen --sort-vars --out ${DNANEXUS}

./plink2 --pfile ${GTAK} --pgen-diff ${DNANEXUS} include-missing --out ${OUT}
The --make-pgen calls seem to working fine, but I get the error when running pgen-diff.

Thank you.

commented

Some REF/ALT alleles are swapped in at least one of your VCFs.

If you don't have any indels, the --ref-from-fa flag can be used to repair the problem VCF. Otherwise, you need to debug something earlier in your pipeline.