Hi Sanjay, I used “Genome studio” for SNP calling, but I am not sure this will fit into your study

 

Cheers

Tamil

 

From: bioinformatics-list-bounces@list.utas.edu.au [mailto:bioinformatics-list-bounces@list.utas.edu.au] On Behalf Of Anna Brueniche-Olsen
Sent: Monday, 1 August 2016 2:01 PM
To: Sanjay Gautam <sanjay.gautam@utas.edu.au>
Cc: bioinformatics-list@list.utas.edu.au
Subject: Re: Variant call tools

 

Hi Sanjay, 

 

GATKs "best practises" tutorials are a good way of getting hold of qc, SNP calling, etc.

 

https://software.broadinstitute.org/gatk/best-practices/

 

Cheers,

Anna


On Jul 31, 2016, at 11:50 PM, Sanjay Gautam <sanjay.gautam@utas.edu.au> wrote:

Hi, 

I am currently working on next generation sequencing platform. I will be pleased to hear if someone in the group could help me get into variant call methods (particularly SNPeff, SAMtools and bcftools platform). 

 

Thank you 

 

 

 

Sanjay Gautam, B.Sc. MLT, M.Sc. Med. Microbiology

PhD Student/School of Medicine/ Breathe Well Center

University of Tasmania, 17 Liverpool Street, Hobart TAS 7000,Australia

 



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