Targeting causative variant in Exome-Sequence data

Question

[sherbuneri10]

Hiii. Anyone there to help me out, how to target causative variant/gene/SNP/INDEL in Exome/seq data?? I have next-gen sequencing data having BAM, vcf files and excel sheet file.

[GenoMax]

Have you looked at snpEff or VEP?

[sherbuneri10]

Sorry I am not getting you

[GenoMax]

Since your original question did not have sufficient detail I thought you were looking for tools to annotate the variants you have.

[WouterDeCoster]

how to target causative variant/gene/SNP/INDEL in Exome/seq data??

Do you mean how to identify causal mutations?

Please elaborate on your experimental setup (e.g. disease, the number of samples,...).

[sherbuneri10]

I have two autosomal recessive male infertility families. I sequenced two individuals of each family . now I need to find the causative variant/mutation in each sample. In total four samples data

[WouterDeCoster]

So essentially you are looking for a filtering strategy and tools to accomplish that? I think a tool such as Gemini might be useful for you.

[sherbuneri10]

Yup I need filtering the variants but I don't know how to do it. I can share the files if you or some one other can give me a favour and help me out

[GenoMax]

That is not how this forum works. People will offer solutions but you are expected to do the analysis yourself. It is good for you in the long run since if you sequence more samples then next time around you would be able to do this without asking us.

[sherbuneri10]

OK thank you so much Dear

[WouterDeCoster]

Your question was rather broad and unclear. If you have more specific questions you will get more specific help. So feel free to come back (and open a new thread) when you need more help during your journey. But be as specific as possible.

Answer 1

[Karma]

In the first step you can annotate your vcf file using Annovar. Annotated variants can be checked against database of ClinVar here

It will show you whether the mutations are pathogenic or not

Thank You