How to find nu. of variants present in a gene for my Exome seq. sample

Question

[bioinf_data-analyst9449]

Dear All, I'm new to NGS and learning bioinformatics analysis in NGS. I have generate vcf file using samtools. I have to find number of variants present in a gene for my NGS sample. I am unable to understand, how to track those variants from vcf wrt. to a particular gene and find the variants.

Please assist me.

thanks in advance.

[GenoMax]

Use vcftools. See the help section here.

[ivivek_ngs]

the easiest way will be to annotate your variants and then scan through the list of gene and output the corresponding variant positions, this way you get the list of variants per gene programmatically. If you want to see it visually then IGV is one option. For annotation, there are multiple tools that will do the trick so you have to select your annotation tool and do the needful.

Answer 1

[prasundutta87]

You can annotate your variants using variant annotation tools such as SnpEff/Annovar/VEP and you can filter your vcf file using your gene of interest to get only those variants that has an effect on your gene of interest..

The second way is what I guess genomax is pointing you towards (correct me if I am wrong)..I'll just explain a little more- if you know the coordinates of your gene (start and end exon coordinates) which you will get from your GTF/GFF file of your reference genome, you can use the position filtering option..