Users reported issues that no SNPs were incorporated when they ran SNPsplit. The issue turned out to be caused by the fact that the Ensembl version of the vcf file uses a chromosome nomenclature like 1, 2, 3, X, Y, MT whereas UCSC uses chr1, chr2, chr3, chrX, chrY, chrM instead. This causes SNPsplit to look up chromosomes that do not actually exist.
Can we add a check to see if the chromosome names appear to be conflicting and make it die horribly.
Users reported issues that no SNPs were incorporated when they ran SNPsplit. The issue turned out to be caused by the fact that the Ensembl version of the
vcffile uses a chromosome nomenclature like1, 2, 3, X, Y, MTwhereas UCSC useschr1, chr2, chr3, chrX, chrY, chrMinstead. This causes SNPsplit to look up chromosomes that do not actually exist.Can we add a check to see if the chromosome names appear to be conflicting and make it die horribly.