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<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="moz-cite-prefix">On 13/05/2019 03:44, Sergey Naumenko
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAPOYbpb_2D=EeBBCbo4L9RLne0S6ELV-_6pRdwbM5--xQKchpg@mail.gmail.com">
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<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">Dear
Ensembl developers!</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px"><br>
</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">Thank
you for all your great work!</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px"><br>
</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">Gnomad
2.1. is a major update of Gnomad database of variation in the
human population </div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">(whole
exome and whole genome sequencing).</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px"><a
href="https://macarthurlab.org/2018/10/17/gnomad-v2-1/"
rel="nofollow" target="_blank" class="gmail-"
style="color:rgb(25,106,212)" moz-do-not-send="true">https://macarthurlab.org/2018/10/17/gnomad-v2-1/</a><br>
</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px"><br>
</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">We are
using Ensembl hosted Gnomad vcf files in cloudbiolinux and
bcbio.</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px"><a
href="https://github.com/chapmanb/cloudbiolinux"
rel="nofollow" target="_blank"
class="enhancr_card_7783636078"
style="color:rgb(25,106,212)" moz-do-not-send="true">chapmanb/cloudbiolinux</a><br>
</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px"><a
href="https://github.com/bcbio/bcbio-nextgen" rel="nofollow"
target="_blank" class="enhancr_card_8460760495"
style="color:rgb(25,106,212)" moz-do-not-send="true">bcbio/bcbio-nextgen</a><br>
</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px"><br>
</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">There is
a difference between gnomad2.0.1 files and gnomad2.1 - they
are split into chromosomes:</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px"><a
href="http://ftp.ensemblorg.ebi.ac.uk/pub/data_files/homo_sapiens/GRCh37/variation_genotype/gnomad/r2.1/exomes/"
rel="nofollow" target="_blank"
class="enhancr_card_7759586661"
style="color:rgb(25,106,212)" moz-do-not-send="true">Index
of
/pub/data_files/homo_sapiens/GRCh37/variation_genotype/gnomad/r2.1/exomes</a><br>
</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px"><br>
</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">To use
gnomad2.1 in the annotation step of bcbio (we annotate with
vcfanno), we decided to merge the files</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">and
remove a number of INFO fields to reduce the file size, see
the discussion here:</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px"><a
href="https://github.com/bcbio/bcbio-nextgen/issues/2736"
rel="nofollow" target="_blank"
class="enhancr_card_8361792277"
style="color:rgb(25,106,212)" moz-do-not-send="true">Using
gnomad2.1: request for opinions · Issue #2736 ·
bcbio/bcbio-nextgen</a><br>
</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px"><br>
</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">We
created recipes in cloudbiolinux to merge gnomad2.1 vcfs for
grch37, grch38, and hg19.<br>
</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px"><a
href="https://github.com/chapmanb/cloudbiolinux/blob/master/ggd-recipes/GRCh37/gnomad.yaml"
rel="nofollow" target="_blank" class="gmail-"
style="color:rgb(25,106,212)" moz-do-not-send="true">https://github.com/chapmanb/cloudbiolinux/blob/master/ggd-recipes/GRCh37/gnomad.yaml</a><br>
</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px"><br>
</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">However,
the long running time makes merging gnomad vcf files in every
local installation not feasible.</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">We
decided to generate merged files once, and then provide users
with easy to install recipe.</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px"><br>
</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">Would
you kindly agree to host merged vcfs for gnomad exome and
genome for grch37 and grch38 on ENSEMBL FTP server?</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px"><br>
</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">We would
be happy to produce the files and upload them.</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">The
technical steps on how we merge the vcfs are listed in the
recipe: </div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">we sort
the variants, filter only PASS variants, keep the pre-defined
subset of INFO fields, etc.</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px"><br>
</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">We hope
that many of Ensembl users would benefit </div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">from the
merged and relatively slim gnomad2.1 vcf files,</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">and we
are happy to share our work with Ensembl.</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px"><br>
</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">Thanks!</div>
<div style="color:rgb(29,34,40);font-family:"Helvetica
Neue",Helvetica,Arial,sans-serif;font-size:13px">Sergey
Naumenko</div>
</div>
<br>
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<pre class="moz-quote-pre" wrap="">_______________________________________________
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