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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