Hello, I am trying to calculate the total number of SNPs in my VCF file. When I tried using Picardtool's CollectVariantCallingMetrics, it calculates 174387 SNPs. However, when I tried to use the command line to calculate my SNPs, I get 199320. The command line I used is as follow:
grep -v "#" VARIANT_VCF | wc -l
Does anyone know why there is a difference in 24933 SNPs called in the 2 calculation methods?
Thank you very much for your help!