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
M +61416181795 / E.mail: Sanjay.Gautam@utas.edu.au



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