<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">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 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">Now when I run it, it appears to complete without error, but I'm running into many of these warnings:</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">Use of uninitialized value in list assignment at /humgen/atgu1/fs03/DM-Lab/vep/ensembl-tools-release-85/scripts/variant_effect_predictor/Bio/EnsEMBL/Variation/Utils/VEP.pm line 5344, <DUMP> line 1.</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">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> <br> <div id="bloop_sign_1475092707093548032" class="bloop_sign"><div style="font-family:helvetica,arial;font-size:13px">-Konrad</div></div> <br><p class="airmail_on">On September 27, 2016 at 10:58:54 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">You can try running it with --verbose, it will give
you some error logging.
<div><br></div>
<div>Will</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">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>
<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 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 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.<wbr>v25lift37.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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