I am currently working on trying to obtain the general statistics on a set of SNPs. I have the original vcf file that I used in Plink to analyze for LD, HWE, etc. I now have a filtered set of SNPs I would like to run through snpEff. Unfortunately, even when I use PGDspider to convert the .ped and .map file back into a .vcf, I have lost the original chromosome names from the original .vcf file as the chromosome ids get changed in the process .vcf to .ped. I need the chromosome id to be the original id so it will correspond to the reference genome in snpEff. Does anyone have any ideas on how to do this? Any help will be appreciated!
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