<div dir="ltr"><div>Thanks, Sarah!</div><div>We will give it a try.</div><div>SN</div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Tue, May 14, 2019 at 9:33 AM Sarah Hunt <<a href="mailto:seh@ebi.ac.uk">seh@ebi.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div bgcolor="#FFFFFF">
<p><br>
</p>
<p>Hi Sergey, <br>
</p>
<p>Thanks for you kind words about Ensembl. <br>
</p>
<p>Ensembl is not an archive - the data files on our FTP site are
used in our services or created from our databases for each
release - so we would not be best placed to host these files. Have
you considered contacting the gnomAD team about hosting your
slimmed down files? <br>
</p>
<p>Best wishes,</p>
<p>Sarah<br>
</p>
<br>
<div class="gmail-m_369832831520029699moz-cite-prefix">On 13/05/2019 03:44, Sergey Naumenko
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Dear
Ensembl developers!</div>
<div><br>
</div>
<div>Thank
you for all your great work!</div>
<div><br>
</div>
<div>Gnomad
2.1. is a major update of Gnomad database of variation in the
human population </div>
<div>(whole
exome and whole genome sequencing).</div>
<div><a href="https://macarthurlab.org/2018/10/17/gnomad-v2-1/" rel="nofollow" class="gmail-m_369832831520029699gmail-" style="color:rgb(25,106,212)" target="_blank">https://macarthurlab.org/2018/10/17/gnomad-v2-1/</a><br>
</div>
<div><br>
</div>
<div>We are
using Ensembl hosted Gnomad vcf files in cloudbiolinux and
bcbio.</div>
<div><a href="https://github.com/chapmanb/cloudbiolinux" rel="nofollow" class="gmail-m_369832831520029699enhancr_card_7783636078" style="color:rgb(25,106,212)" target="_blank">chapmanb/cloudbiolinux</a><br>
</div>
<div><a href="https://github.com/bcbio/bcbio-nextgen" rel="nofollow" class="gmail-m_369832831520029699enhancr_card_8460760495" style="color:rgb(25,106,212)" target="_blank">bcbio/bcbio-nextgen</a><br>
</div>
<div><br>
</div>
<div>There is
a difference between gnomad2.0.1 files and gnomad2.1 - they
are split into chromosomes:</div>
<div><a href="http://ftp.ensemblorg.ebi.ac.uk/pub/data_files/homo_sapiens/GRCh37/variation_genotype/gnomad/r2.1/exomes/" rel="nofollow" class="gmail-m_369832831520029699enhancr_card_7759586661" style="color:rgb(25,106,212)" target="_blank">Index
of
/pub/data_files/homo_sapiens/GRCh37/variation_genotype/gnomad/r2.1/exomes</a><br>
</div>
<div><br>
</div>
<div>To use
gnomad2.1 in the annotation step of bcbio (we annotate with
vcfanno), we decided to merge the files</div>
<div>and
remove a number of INFO fields to reduce the file size, see
the discussion here:</div>
<div><a href="https://github.com/bcbio/bcbio-nextgen/issues/2736" rel="nofollow" class="gmail-m_369832831520029699enhancr_card_8361792277" style="color:rgb(25,106,212)" target="_blank">Using
gnomad2.1: request for opinions · Issue #2736 ·
bcbio/bcbio-nextgen</a><br>
</div>
<div><br>
</div>
<div>We
created recipes in cloudbiolinux to merge gnomad2.1 vcfs for
grch37, grch38, and hg19.<br>
</div>
<div><a href="https://github.com/chapmanb/cloudbiolinux/blob/master/ggd-recipes/GRCh37/gnomad.yaml" rel="nofollow" class="gmail-m_369832831520029699gmail-" style="color:rgb(25,106,212)" target="_blank">https://github.com/chapmanb/cloudbiolinux/blob/master/ggd-recipes/GRCh37/gnomad.yaml</a><br>
</div>
<div><br>
</div>
<div>However,
the long running time makes merging gnomad vcf files in every
local installation not feasible.</div>
<div>We
decided to generate merged files once, and then provide users
with easy to install recipe.</div>
<div><br>
</div>
<div>Would
you kindly agree to host merged vcfs for gnomad exome and
genome for grch37 and grch38 on ENSEMBL FTP server?</div>
<div><br>
</div>
<div>We would
be happy to produce the files and upload them.</div>
<div>The
technical steps on how we merge the vcfs are listed in the
recipe: </div>
<div>we sort
the variants, filter only PASS variants, keep the pre-defined
subset of INFO fields, etc.</div>
<div><br>
</div>
<div>We hope
that many of Ensembl users would benefit </div>
<div>from the
merged and relatively slim gnomad2.1 vcf files,</div>
<div>and we
are happy to share our work with Ensembl.</div>
<div><br>
</div>
<div>Thanks!</div>
<div>Sergey
Naumenko</div>
</div>
<br>
<fieldset class="gmail-m_369832831520029699mimeAttachmentHeader"></fieldset>
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