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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?

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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

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  • $\begingroup$ thanks, I will try that! $\endgroup$ – user6720 Jan 6 at 16:08

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