kaichop
commented
2 years ago D is not a valid allele. you can delete this SNP (which is not mapped to chromosome either) from your files and try again.
On Wed, Dec 22, 2021 at 9:00 PM zoeward-nz @.***> wrote:
I am using Illumina GSA-24v3-0 chip and have followed the tutorial to make the SNPTable. When I try to run convert_bim.pl with -intype top (which I believe it is) I get the Error: invalid alleles found in BIM file (the -intype of 'top' indicates possible alleles as ACGT0): <0 rs111033319 0 0 0 D>
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I am using Illumina GSA-24v3-0 chip and have followed the tutorial to make the SNPTable. When I try to run convert_bim.pl with -intype top (which I believe it is) I get the Error: invalid alleles found in BIM file (the -intype of 'top' indicates possible alleles as ACGT0): <0 rs111033319 0 0 0 D>