In working with the ROSMAP imputed genotype data (Rush-Broad AffymetrixGeneChip_imputed), I have noted that in the specific chromosome dosage files, that there are SNPs which are not located on that particular chromosome, by reference to dbSNP (dbSNP 150). For example, for chromosome 11 (syn 5879748.1), the snps rs2202718 are identified as located on chromosome 3 and rs72488967 is on chromosome 4. Why would this be the case? Is there a way to filter the results to limit to the specific chromosome that corresponds to the label of the dosage file? Thanks.
Created by Michael Lutz NCTrailRunner @NCTrailRunner -
It seems likely that someone lifted over the SNP locations from one genome build to another, but did not re-sort the SNPs into the respective files. Plink has functions for selecting markers by chromosome, so would be your best bet for pruning out these SNPs.
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