<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hello Jan,<div><br></div><div>we used the pipeline described in /ensembl-variation/documentation/README.snp.calling.txt to call SNPs for a variety</div><div>of species (e.g. human, rat, zebrafish, mouse, …). The pipeline is stable and computes sensible results. </div><div><br></div><div>We recently tried new approaches for calling SNPs which included using bwa for aligning reads and samtools and bcftools</div><div>for SNP calling. One of the main advantages is a huge decrease in running time. I can add a documentation for the new pipeline</div><div>in the next release.</div><div><br></div><div>Maybe you should have a look at how the 1000 genomes project calls SNPs as well: <a href="http://www.1000genomes.org/analysis">http://www.1000genomes.org/analysis</a></div><div><br></div><div>Regards,</div><div>Anja</div><div><br></div><div><div>On 12 Feb 2013, at 15:43, Jan Vogel wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hello Ensembl, <br><br>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". <br><br>I read through "Ensembl variation resources" (<a href="http://www.biomedcentral.com/1471-2164/11/293">http://www.biomedcentral.com/1471-2164/11/293</a>) and also checked <br>out the ensembl-variation/documentation/README.snp.calling.txt in CVS.<br><br>Is this pipeline still in use ? And can you point me to other resources on the Ensembl SNP pipeline ? <br><br>Thanks, <br><br> Jan Vogel</div>_______________________________________________<br>Dev mailing list <a href="mailto:Dev@ensembl.org">Dev@ensembl.org</a><br>Posting guidelines and subscribe/unsubscribe info: <a href="http://lists.ensembl.org/mailman/listinfo/dev">http://lists.ensembl.org/mailman/listinfo/dev</a><br>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><br></blockquote></div><br></body></html>