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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$\begingroup$ Using SnpEff (snpeff.sourceforge.net/SnpEff_manual.html#databases) you can build custom annotation databases using the gff or gtf file. VEP also offers similar functionality asia.ensembl.org/info/docs/tools/vep/script/vep_custom.html. $\endgroup$– arupCommented Jan 6, 2020 at 9:58
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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
