Using SNPRelate Results to prune VCF files

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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Using SNPRelate Results to prune VCF files #51

Closed TrinityConn closed 5 years ago

TrinityConn commented 5 years ago

I am new to using SNPRelate to analyze my data --- I pruned my SNPS for LD and want to filter my original VCF files according to the pruned data set from SNPRelate (for further use in other programs). However, the SNP ids coming out of SNPRelate are obviously not the same format --- is there a way to reformat the snpset.ids coming out of SNPRelate so I can use it as a single line document to filter through vcf/bcf tools?

zhengxwen commented 5 years ago

If you used VCF/BCF, would you please try SeqArray?