Question: Help NGS data analysis
0
gravatar for bercelin.maniangou
3.5 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 3.5 years ago by Guy Reeves1.0k • written 3.5 years ago by bercelin.maniangou0
0
gravatar for Guy Reeves
3.5 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 3.5 years ago by Guy Reeves1.0k
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