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zhengxwen / SNPRelate

R package: parallel computing toolset for relatedness and principal component analysis of SNP data (Development version only)
http://www.bioconductor.org/packages/SNPRelate
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Chromosome codes with GWASTools #7

Open zhengxwen opened 10 years ago

zhengxwen commented 10 years ago

Does snpgdsBED2GDS do any conversion of the chromosome codes in the PLINK file? PLINK has 24=Y and 25=XY, while GWASTools assumes 24=XY and 25=Y. Could you add this option if it doesn't exist already?

thanks, Stephanie

zhengxwen commented 9 years ago

GWASTools (<= v1.13.3) requires integer chromosome ids, as well as integer snp.id.