bedtool intersect to compare .vcf file to reference genome I have a .vcf file generated using samtools. I want to know mutations in specific genes by comparing .vcf files with a reference genome. I cannot use the Ensembl VEP tool as my reference genome is not listed there. Can you please help?
If you want to filter a VCF file, you might want to give VCFtools a try.

Here is the documentation : VCFtools Manual

I am not a specialist of this tool but you could do as the following. First build a bedfile with the chromosome names and positions of your genes (start and stop) such as this :

chr   start   stop   (name)   (score)   (strand)


Then it should work with this command line :

vcftools --vcf file.vcf --bed positions.bed --out filtered.vcf


The output will be a VCF filtered on the provided regions