<html><head><style>body{font-family:Helvetica,Arial;font-size:13px}</style></head><body style="word-wrap:break-word"><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">Hmm, that's interesting. When I added info.txt, now everything failed with:</div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto"><br></div><div id="bloop_customfont" style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">Can't call method "db" on unblessed reference at /humgen/atgu1/fs03/DM-Lab/vep/ensembl-tools-release-85/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/TranscriptVariation.pm line 324.</div> <br> <div id="bloop_sign_1475160496850545920" class="bloop_sign"><div style="font-family:helvetica,arial;font-size:13px">-Konrad</div></div> <br><p class="airmail_on">On September 29, 2016 at 9:34:18 AM, Will McLaren (<a href="mailto:wm2@ebi.ac.uk">wm2@ebi.ac.uk</a>) wrote:</p> <blockquote type="cite" class="clean_bq"><span><div><div></div><div>
<title></title>
<div dir="ltr">We might be able to write a plugin to read the data
from a pair of table dump files.
<div><br>
Let me have a go at doing that, as you are not the only person
requesting similar at the moment!</div>
<div><br></div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On 29 September 2016 at 14:21, Konrad
Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org" target="_blank">konradk@broadinstitute.org</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
Great, thanks! Will check that out.</div>
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
<br></div>
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
Is that to say there's no way to get the SIFT and PolyPhen
annotations locally? Happy to do some legwork if it means I can
recreate the entire thing with this new annotation set!</div>
<span class="HOEnZb"><font color="#888888"><br></font></span>
<div>
<div style="font-family:helvetica,arial;font-size:13px">
<span class="HOEnZb"><font color="#888888">-Konrad</font></span></div>
</div>
<div>
<div class="h5"><br>
<p>On September 29, 2016 at 3:52:47 AM, Will McLaren (<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>)
wrote:</p>
<blockquote type="cite">
<div>
<div>
<div dir="ltr"><span>You'd also need to copy over the
homo_sapiens/85_GRCh37/info.<wbr>txt file, this contains the
column headers for the _var files, hence the warnings when it finds
data that doesn't match its best guess of those headers.</span>
<div><span><br></span></div>
<div><span>RE: SIFT and PolyPhen, if you use --cache instead of
--offline you *might* find that it is able to retrieve SIFT and
PolyPhen matrices from the database server. I've tested this with
the new code but not the version you're on. You might also want to
use "--host <a href="http://useastdb.ensembl.org" target="_blank">useastdb.ensembl.org</a>", assuming you're East Coast,
this will give you the fastest (public) DB connection.</span></div>
<div><span><br></span></div>
<div><span>Will</span></div>
</div>
<div class="gmail_extra"><span><br></span>
<div class="gmail_quote"><span>On 28 September 2016 at 21:00,
Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org" target="_blank">konradk@broadinstitute.org</a>></span>
wrote:<br></span>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
Ok, I think I got that mostly working (sorted it properly and
converted transcript_type to transcript_biotype, appears to have
worked). I then pulled the _var and _reg caches over as-is from 85
(not sure if wise).</div>
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
<br></div>
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
Now when I run it, it appears to complete without error, but I'm
running into many of these warnings:</div>
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
<br></div>
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
Use of uninitialized value in list assignment at
/humgen/atgu1/fs03/DM-Lab/vep/<wbr>ensembl-tools-release-85/scrip<wbr>ts/variant_effect_predictor/<wbr>Bio/EnsEMBL/Variation/Utils/<wbr>VEP.pm
line 5344, <DUMP> line 1.</div>
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
<br></div>
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
Also, SIFT and PolyPhen don't appear to get output alongside it. Is
that expected (or perhaps related to above warnings)? Anything I
can do to get those in there?</div>
<span><font color="#888888"><br></font></span>
<div>
<div style="font-family:helvetica,arial;font-size:13px">
<span><font color="#888888">-Konrad</font></span></div>
</div>
<div>
<div><br>
<p>On September 27, 2016 at 10:58:54 AM, Will McLaren (<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>)
wrote:</p>
<blockquote type="cite">
<div>
<div>
<div dir="ltr"><span>You can try running it with --verbose, it will
give you some error logging.</span>
<div><span><br></span></div>
<div><span>Will</span></div>
</div>
<div class="gmail_extra"><span><br></span>
<div class="gmail_quote"><span>On 27 September 2016 at 15:56,
Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org" target="_blank">konradk@broadinstitute.org</a>></span>
wrote:<br></span>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
Ok good to know - I actually tried it, but I think something is
being odd. It gets through the whole thing (going back and forth
between chromosomes like you said, so I can try to fix that), but
then appears to finish:</div>
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
<br></div>
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
<div style="margin:0px">2016-09-26 16:12:30 - Processing chromosome
Y</div>
<div style="margin:0px">WARNING: Could not find chromosome named M
in FASTA file</div>
<div style="margin:0px">2016-09-26 16:12:52 - All done!</div>
<div style="margin:0px"><br></div>
<div style="margin:0px">But the output directory (either ~/.vep or
the directory I pointed to with --dir) are empty. Is this a related
issue? Thought you might want to know to add a bit of error logging
if so.</div>
</div>
<span><font color="#888888"><br></font></span>
<div>
<div style="font-family:helvetica,arial;font-size:13px">
<span><font color="#888888">-Konrad</font></span></div>
</div>
<div>
<div><br>
<p>On September 27, 2016 at 8:30:15 AM, Will McLaren (<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>)
wrote:</p>
<blockquote type="cite">
<div>
<div>
<div dir="ltr"><span>In theory this should work, but the <a href="http://gtf2vep.pl" target="_blank">gtf2vep.pl</a> script doesn't
seem to work too well with this particular GFF (it was designed
really to work with GFF/GTFs as produced by Ensembl or NCBI).
Probably with some tweaks it could be made to work - I believe the
major issues are caused by features being out of the order that the
script expects.</span>
<div><span><br></span></div>
<div><span>The new code uses a much more robust system for
constructing transcripts and has been tested with GFFs from
Ensembl, NCBI and GENCODE.</span></div>
<div><span><br></span></div>
<div><span>Will</span></div>
</div>
<div class="gmail_extra"><span><br></span>
<div class="gmail_quote"><span>On 27 September 2016 at 13:22,
Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org" target="_blank">konradk@broadinstitute.org</a>></span>
wrote:<br></span>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
I just also realized - would creating a cache from this gff file
(using <a href="http://gtf2vep.pl" target="_blank">gtf2vep.pl</a>)
not be recommended?</div>
<span><font color="#888888"><br></font></span>
<div>
<div style="font-family:helvetica,arial;font-size:13px">
<span><font color="#888888">-Konrad</font></span></div>
</div>
<div>
<div><br>
<p>On September 27, 2016 at 5:16:42 AM, Will McLaren (<a href="mailto:wm2@ebi.ac.uk" target="_blank">wm2@ebi.ac.uk</a>)
wrote:</p>
<blockquote type="cite">
<div>
<div>
<div dir="ltr"><span>Hi Konrad,</span>
<div><span><br></span></div>
<div><span>The beta ensembl-vep code [1] supports annotation
directly from a GFF file, such as the one available from the
GENCODE website [2].</span></div>
<div><span><br></span></div>
<div><span>$ curl <a href="ftp://ftp.sanger.ac.uk/pub/gencode/Gencode_human/release_25/GRCh37_mapping/gencode.v25lift37.annotation.gff3.gz" target="_blank">ftp://ftp.sanger.ac.uk/pu<wbr>b/gencode/Gencode_human/releas<wbr>e_25/GRCh37_mapping/gencode.v2<wbr>5lift37.annotation.gff3.gz</a>
| gzip -dc | grep -v "#" | sort -k1,1 -k4,4n -k5,5n | bgzip -c >
gencode.v25lift37.annotation.g<wbr>ff3.gz</span></div>
<div><span>$ tabix -p gff
gencode.v25lift37.annotation.g<wbr>ff3.gz</span></div>
<div><span>$ perl <a href="http://vep.pl" target="_blank">vep.pl</a> -i variants.vcf
-gff gencode.v25lift37.annotat<wbr>ion.gff3.gz -fasta
homo_sapiens.fa</span></div>
<div><span><br></span></div>
<div><span>This comes with limitations as the GFF file contains
only the transcript structure and not any of the additional
annotations. However I do know of someone successfully using LOFTEE
with this exact setup.</span></div>
<div><span><br></span></div>
<div><span>Of course usual beta caveats apply, so if you do use it
and find bugs please report on the GitHub page.</span></div>
<div><span><br></span></div>
<div><span>Regards</span></div>
<div><span><br></span></div>
<div><span>Will McLaren</span></div>
<div><span>Ensembl Variation</span></div>
<div><span><br></span></div>
<div><span>[1] : <a href="https://github.com/willmclaren/ensembl-vep" target="_blank">https://github.com/willmclar<wbr>en/ensembl-vep</a></span></div>
<div><span>[2] : <a href="http://www.gencodegenes.org/releases/25lift37.html" target="_blank">http://www.gencodegenes.org/<wbr>releases/25lift37.html</a></span></div>
</div>
<div class="gmail_extra"><span><br></span>
<div class="gmail_quote"><span>On 26 September 2016 at 20:40,
Konrad Karczewski <span dir="ltr"><<a href="mailto:konradk@broadinstitute.org" target="_blank">konradk@broadinstitute.org</a>></span>
wrote:<br></span>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
Hi all,</div>
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
<br></div>
<div style="font-family:Helvetica,Arial;font-size:13px;color:rgba(0,0,0,1.0);margin:0px;line-height:auto">
When running VEP 85 on GRCh37, I believe the process has been to
annotate against Gencode 19 (the info.txt seems to confirm this).
Realizing the ridiculousness of my request, is there any chance
there is a cache floating around for Gencode 25lift37? Would go a
long way for ExAC releases. </div>
<div><br></div>
Thanks!<span><font color="#888888"><br></font></span>
<div>
<div style="font-family:helvetica,arial;font-size:13px">
<span><font color="#888888">-Konrad</font></span></div>
</div>
</div>
<br>
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