I have used dbSNP build 138 to tag 'rs' ID in my VCF file. But later I came to know that now dbSNP build 150 has been released. I want to update the rs IDs in my VCF file.
I tried but I found a problem for which I need suggestion. With dbSNP build 138, I am getting 450076 total variants, 248236 as known variants and the rest as novel. But when I use the latest dbSNP file,
All_20170710.vcf.gz, I am getting same total variants but 0 as known and all as novel which is definitely wrong.
When I checked the reason for this, I found that in the
All_20170710.vcf.gz VCF file, all chromosomes are written as numbers like
2, instead of
chr2 while in my vcf file, all chromosomes are written as
chr2. The dbSNP build 138 file also has the chromosome names with the
chr prefix, and that's why 138th build was giving good results.
One solution would be add the
chr word before chromosome number. Is that an efficient way? How do I do that? If not, what is the correct way to use the latest dbSNP
All_20170710.vcf.gz to tag rs IDs in a vcf file which contains ~32 Billion SNPs instead of
dbsnp_138.vcf which contains only ~6 Billion SNPs? Any suggestions??