[BioC] SNP detection of multiple samples

[Wang, Li]

Hi, Paul

Thanks for your reply. I will look into those packages and select the suitable one for exploration.

Cheers
Li
________________________________________
From: Paul Leo [p.leo at uq.edu.au]
Sent: Wednesday, May 23, 2012 11:45 PM
To: Wang, Li
Cc: bioconductor at r-project.org
Subject: Re: [BioC] SNP detection of multiple samples

Think you are better off using something "like" GATK -which has a
Bayesian algorithm where you get more power to detect SNPs by adding
more samples.

FYI Since you have transcriptones you might have to watch standed-ness
issues depending  on the expt protocol you have. ...

That said samtools mpileup will probably work just as well and even
vcftools with a simple vcf merge may even be all you need?

Those hi-throughput "workhorse" packages will probably be better for
such a task. We use bioconductor extensively for NGS analysis but not
the SNP/indel calling specifically.

Rsamtools has an R interface to many of these operations and you will
also need to understand the GenomicFeatures package to get full benefit.

Cheers
Paul







-----Original Message-----
From: Wang, Li <li.wang at ttu.edu>
To: bioconductor at r-project.org <bioconductor at r-project.org>
Subject: [BioC] SNP detection of multiple samples
Date: Wed, 23 May 2012 16:29:54 -0500

Hi, all

I have transcriptomes of 31 samples. I have detected SNPs for each sample compared to Reference genome.

My goal is to detect common SNPs among all the 31 samples based on 31 tables of SNPs (each sample vs reference genome).

I am writing to ask if there is a bioconductor package which can achieve my goal.

Thanks!

Li
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