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.aumailto: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 M +61416181795tel:%2B61416181795 / E.mail: Sanjay.Gautam@utas.edu.aumailto:Sanjay.Gautam@utas.edu.au
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