I am trying to merge a bunch of vcf files into one vcf of known SNPs. The files are separated by chromosome. I am trying to figure out how to merge all the files but in a way that the chromosome number stays intact.. if that makes sense? I want to use this file with GATK so I don't just a bunch of mixed up merged vcf files.
I know there are a number of tools like vcf-merge, bcftools-merge, and GATK's CombineVariants
Does any one know which software would work best?
Also, does anyone have any suggestions/know and site that will have known SNP or indels? I got this first batch of vcf files from dbSNP