I'd recommend you look at our suite of tools, called the GATK, for
working with NGS data. It includes a very useful test of tools for
comparing and evaluating SNP call quality:
On Jul 9, 2010, at 4:45 AM, Nicola Nadeau wrote:
I am trying to find SNPs and/or indel variants that differ between two
groups of samples. The data are 454 sequence capture results
region of interest for a non-model organism without a complete
have mapped these to my reference sequence of the region and generated
BAM and pileup files for them. Does anyone know of a tool or method
(either in galaxy or elsewhere) that will allow me to compare datasets
and pick out variation between them (as opposed to things that differ
from the reference sequence).
galaxy-user mailing list
Mark A. DePristo, Ph.D.
Manager, Medical and Population Genetics Analysis
Broad Institute of Harvard and MIT