I have successfully managed to run SnpEff for my vcf files. However, the count of missense variants in my html file and the VCF file generated by SnpEff are different.
Missense in HTML: 205,104 Missense in VCF fle: 190,605
Can any one please suggest me about the criteria for missense calculation in html file, so that I could match the vcf file with the missense file.
My SnpEff version is: 4.1 Genome used: rice7 Command Line: snpEff ann -V rice7 [input_file]