Question: Help NGS data analysis
0
gravatar for bercelin.maniangou
3.6 years ago by
France
bercelin.maniangou0 wrote:

Dear all,

I am working on the NGS data by using some galaxy tools and I do not know many things on bioinformatics. The aim of my project is to type KIR genes at the allelic level. Those genes are very polymorphic like HLA genes. Now, I used BWA-MEM to align my illumina paired end reads to the human reference genome hg19 and try to visualized them on IGV but I do not know which galaxy tool should I use after to identify the different alleles for each gene. I read on the internet that after alignment, the next step is the calling variant but i do not know what tool for that...

Thank u in advance,

BM

 

ADD COMMENTlink modified 3.6 years ago by Guy Reeves1.0k • written 3.6 years ago by bercelin.maniangou0
0
gravatar for Guy Reeves
3.6 years ago by
Guy Reeves1.0k
Germany
Guy Reeves1.0k wrote:

Hi BM

There are a number of very readable resources out there to help with the bewildering number of choices you need to make at the neighing , this link to a previous question I think gives two of the best.

A: How to use GATK on Galaxy

I suspect you will also  opt for GATK for variant calling 

Once you have a basic plan (and maybe a workflow to go with it), this forum is a great place to come back to for specific questions.

Thanks  Guy

ADD COMMENTlink written 3.6 years ago by Guy Reeves1.0k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 171 users visited in the last hour