Question: Targeting causative variant in Exome-Sequence data
0
gravatar for sherbuneri10
2.8 years ago by
sherbuneri100 wrote:

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.

snp • 1.1k views
ADD COMMENTlink modified 2.8 years ago by Karma270 • written 2.8 years ago by sherbuneri100
1

Have you looked at snpEff or VEP?

ADD REPLYlink written 2.8 years ago by genomax83k

Sorry I am not getting you

ADD REPLYlink written 2.8 years ago by sherbuneri100

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

ADD REPLYlink written 2.8 years ago by genomax83k

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,...).

ADD REPLYlink written 2.8 years ago by WouterDeCoster43k

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

ADD REPLYlink written 2.8 years ago by sherbuneri100

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.

ADD REPLYlink written 2.8 years ago by WouterDeCoster43k

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

ADD REPLYlink written 2.8 years ago by sherbuneri100

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.

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by genomax83k

OK thank you so much Dear

ADD REPLYlink written 2.8 years ago by sherbuneri100

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.

ADD REPLYlink written 2.8 years ago by WouterDeCoster43k
2
gravatar for Karma
2.8 years ago by
Karma270
India
Karma270 wrote:

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

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Karma270
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