[ensembl-dev] Info/Doc on the Ensembl SNP pipeline?

Anja Thormann anja at ebi.ac.uk
Wed Feb 13 14:19:43 GMT 2013

Hello Jan,

we used the pipeline described in /ensembl-variation/documentation/README.snp.calling.txt to call SNPs for a variety
of species (e.g. human, rat, zebrafish, mouse, …). The pipeline is stable and computes sensible results. 

We recently tried new approaches for calling SNPs which included using bwa for aligning reads and samtools and bcftools
for SNP calling. One of the main advantages is a huge decrease in running time. I can add a documentation for the new pipeline
in the next release.

Maybe you should have a look at how the 1000 genomes project calls SNPs as well: http://www.1000genomes.org/analysis


On 12 Feb 2013, at 15:43, Jan Vogel wrote:

> Hello Ensembl, 
> I'd like to find out more on how Ensembl calls SNP's. I've got FASTQ files which I would like to align against the human genome to call SNPs, mainly as a "proof of concept". 
> I read through "Ensembl variation resources" (http://www.biomedcentral.com/1471-2164/11/293) and also checked 
> out the ensembl-variation/documentation/README.snp.calling.txt in CVS.
> Is this pipeline still in use ? And can you point me to other resources on the Ensembl SNP pipeline ? 
> Thanks, 
>   Jan Vogel
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