Error when following Genomes1000.Rmd commands

[dpcc2]

When attempting the final step to convert the files from Plink2 to Plink1 format, you receive the following error:

Error: all_phase3.bim cannot contain multiallelic variants

[HannahVMeyer]

PLINK2 allows multi-allelic SNPs, which PLINK1 doesn't. When converting to plink1 format we've got to exclude multi-allelic SNPs with the --max-alleles flag described here: Number of distinct alleles. Fixed in the vignette.

[dpcc2]

?Hi Hannah, Thanks for addressing this issue and getting back to me. Best, Daniel Considine

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________________________________ From: HannahVMeyer <notifications@github.com> Sent: 30 July 2019 20:34 To: HannahVMeyer/plinkQC Cc: Daniel Considine; Author Subject: Re: [HannahVMeyer/plinkQC] Error when following Genomes1000.Rmd commands (#10) PLINK2 allows multi-allelic SNPs, which PLINK1 doesn't. When converting to plink1 format we've got to exclude multi-allelic SNPs with the --max-alleles flag described here: Number of distinct alleles<https://www.cog-genomics.org/plink/2.0/filter#max-alleles>. Fixed in the vignette. - You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#10>, or mute the thread<https://github.com/notifications/unsubscribe-auth/AIGZPMS3NQEZKLCD4CUPMFLQCCJUFANCNFSM4H7RJ2HQ>.