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Old 02-19-2013, 11:10 AM   #9
bpb9
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Location: NYC

Join Date: Aug 2012
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After having made the plink files from the VCF file, I tried to split them up by chromosome in plink but encountered the following error:

ERROR: Locus has >2 alleles:
individual has genotype [ G 0 ]
but we've already seen [ G ] and [ A ]

I thought 0 indicated a monomorphic SNP. I am very confused. I suppose I could try splitting up the vcf file by chromosome in vcftools and then converting to plink, but I don't see why that would get around the above issue. Would it help to recode only biallelic SNPs to plink format instead of all biallelic loci? Is there a way to do that? Any input is appreciated!
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