<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi<div><br></div><div>Is it possible to get minor allele frequencies from 1000 genomes using the Ensembl REST service?</div><div><br></div><div>Thanks</div><div><br></div><div>Rebecca</div><div><br><div><div>On 9 May 2014, at 10:38, Will McLaren <<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr">Hi Rebecca,<div><br></div><div>Have you considered using the Ensembl VEP?</div><div><br></div><div>It can annotate your VCF files with frequency data from 1000 genomes, as well as a lot more:</div><div><br></div>
<div><a href="http://www.ensembl.org/vep">http://www.ensembl.org/vep</a><br></div><div><br></div><div>With the added bonus of no coding required :-)<br><br>If you do still want to do this in Perl, you can retrieve the global (ie combined across populations) frequency from a variation feature object in our Perl API:</div>
<div><br></div><div><a href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#genome">http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#genome</a><br></div><div><br></div><div>or frequencies from any sub-population via allele objects:</div>
<div><br></div><div><a href="http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#alleles">http://www.ensembl.org/info/docs/api/variation/variation_tutorial.html#alleles</a><br></div><div><br></div><div>
Hope that helps</div><div><br></div><div>Will McLaren</div><div>Ensembl Variation</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 9 May 2014 10:28, Rebecca Ewing <span dir="ltr"><<a href="mailto:rpe@sanger.ac.uk" target="_blank">rpe@sanger.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Laura<br>
<br>
I want to search using data in vcf files from our pipeline and to add the information to the files, and I wondered if there was a better way than downloading all of the files.<br>
<br>
Thanks<br>
<span class="HOEnZb"><font color="#888888"><br>
Rebecca<br>
</font></span><div class="HOEnZb"><div class="h5"><br>
On 9 May 2014, at 10:24, Laura Clarke <<a href="mailto:laura@ebi.ac.uk">laura@ebi.ac.uk</a>> wrote:<br>
<br>
> Hi Rebecca<br>
><br>
> You can get the allele frequencies from Ensembl but you may find it<br>
> easier to get the numbers from the 1000 Genomes VCF files<br>
><br>
> <a href="ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/ALL.wgs.integrated_phase1_v3.20101123.snps_indels_sv.sites.vcf.gz" target="_blank">ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/integrated_call_sets/ALL.wgs.integrated_phase1_v3.20101123.snps_indels_sv.sites.vcf.gz</a><br>
><br>
> thanks<br>
><br>
> Laura<br>
><br>
> On 9 May 2014 10:19, Rebecca Ewing <<a href="mailto:rpe@sanger.ac.uk">rpe@sanger.ac.uk</a>> wrote:<br>
>>> Hi<br>
>>><br>
>>> I am writing some perl code to compare some of our data against 1000 genomes and get the minor allele frequencies. What would be the most efficient way to do this?<br>
>>><br>
>>> Thanks<br>
>>><br>
>>> Rebecca<br>
>><br>
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