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Hello Will,<br>
<br>
That's just awesome !<br>
<br>
Thank you.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 04/30/2014 11:42 AM, Will McLaren
wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX1kE9w+3nQyRR5pg7fq-Xwy004S++iWxE-VQTOuYK6NKA@mail.gmail.com"
type="cite">
<div dir="ltr">This was easier to fix than I thought it would be;
I've pushed a fix to the ensembl-variation GitHub repo, it's
available on the release/75 branch.
<div><br>
</div>
<div>Will</div>
</div>
<div class="gmail_extra">
<br>
<br>
<div class="gmail_quote">On 30 April 2014 10:32, mag <span
dir="ltr"><<a moz-do-not-send="true"
href="mailto:mr6@ebi.ac.uk" target="_blank">mr6@ebi.ac.uk</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000"> Hi Will,<br>
<br>
Chromosomes in Ensembl have a 'karyotype_rank' attribute
that gives the expected chromosome ordering (1-22, X, Y,
MT)<br>
<br>
I don't know how applicable it is to VEP, but it might be
something to bear in mind.<br>
<br>
<br>
Cheers,<br>
mag
<div>
<div class="h5"><br>
<br>
<div>On 30/04/2014 09:18, Will McLaren wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Guillermo,
<div><br>
</div>
<div>Currently the VEP internally sorts each
buffer of 5000 variants that it reads in before
writing the output. The sort is done
alphanumerically, so it will order e.g.
1-22,M,X,Y.</div>
<div><br>
</div>
<div>It looks like the buffer partially overlaps
your input groups, such that, in your example,
the first buffer read would be</div>
<div><br>
</div>
<div><span
style="font-family:arial,sans-serif;font-size:13px">chrX
variant1</span><br
style="font-family:arial,sans-serif;font-size:13px">
<span
style="font-family:arial,sans-serif;font-size:13px">chrX
variant2</span><br>
</div>
<div><span
style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div>
<div><span
style="font-family:arial,sans-serif;font-size:13px">These
are parsed, sorted and written out. Then the
buffer reads in the next batch:</span></div>
<div><span
style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div>
<div><span
style="font-family:arial,sans-serif;font-size:13px">chrX
variant3</span><br
style="font-family:arial,sans-serif;font-size:13px">
<span
style="font-family:arial,sans-serif;font-size:13px">chrX
variant4</span><br
style="font-family:arial,sans-serif;font-size:13px">
<span
style="font-family:arial,sans-serif;font-size:13px">chrM
variant1</span><br
style="font-family:arial,sans-serif;font-size:13px">
<span
style="font-family:arial,sans-serif;font-size:13px">chrM
variant2</span><span
style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div>
<div><span
style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div>
<div><font face="arial, sans-serif">which then get
sorted to</font></div>
<div><font face="arial, sans-serif"><br>
</font></div>
<div> <span
style="font-family:arial,sans-serif;font-size:13px">chrM
variant1</span><br
style="font-family:arial,sans-serif;font-size:13px">
<span
style="font-family:arial,sans-serif;font-size:13px">chrM
variant2</span><br
style="font-family:arial,sans-serif;font-size:13px">
<span
style="font-family:arial,sans-serif;font-size:13px">chrX
variant3</span><br
style="font-family:arial,sans-serif;font-size:13px">
<span
style="font-family:arial,sans-serif;font-size:13px">chrX
variant4</span><font face="arial, sans-serif"><br>
</font></div>
<div><span
style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div>
<div><span
style="font-family:arial,sans-serif;font-size:13px">since
M is before X alphabetically. So, I'm afraid
this explains but doesn't fix your problem!
You could ensure that your chrM variants
appear before your chrX and chrY variants in
the file, and this problem shouldn't appear.</span></div>
<div><span
style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div>
<div><font face="arial, sans-serif">For the next
VEP release I'll look into retaining the input
sorting when using VCF as the output format as
I think this would be preferable for most
users.</font></div>
<div><font face="arial, sans-serif"><br>
</font></div>
<div><font face="arial, sans-serif">Regards</font></div>
<div><font face="arial, sans-serif"><br>
</font></div>
<div><font face="arial, sans-serif">Will McLaren</font></div>
<div><font face="arial, sans-serif">Ensembl
Variation</font></div>
</div>
<div class="gmail_extra"><br>
<br>
<div class="gmail_quote">On 30 April 2014 07:47,
Guillermo Marco Puche <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:guillermo.marco@sistemasgenomicos.com"
target="_blank">guillermo.marco@sistemasgenomicos.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0
0 0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000066"> Dear
developers,<br>
<br>
I'm experiencing a strange behavior when
annotating a full sorted VCF file.<br>
My chr order is the following: chr1 to
chr22, chrX, chrY, chrM.<br>
<br>
I've noticed when I've variants in chrX then
in chrM the vep scripts annotates the full
vcf file but it changes the order of some of
the lines. See example below:<br>
<br>
Imagine I've the following variants in my
vcf:<br>
<br>
chrX variant1<br>
chrX variant2<br>
chrX variant3<br>
chrX variant4<br>
chrM variant1<br>
chrM variant2<br>
<br>
After annotating the VCF the order remains
like this:<br>
<br>
chrX variant1<br>
chrX variant2<br>
chrM variant1<br>
chrM variant2<br>
chrX variant3<br>
chrX variant4<br>
<br>
This is just a graphical example. I would
like to fix this, because it's a bit tricky
to get a non sorted VCF annotated file. I've
not experienced this issue with other chrX
and chrM. Already tried to debug this
disabling all the plugins and the issue
reproduces itself.<br>
<br>
Thank very much.<br>
<br>
Best regards,<br>
Guillermo.<br>
</div>
<br>
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<br>
<div class="moz-signature">-- <br>
<title>Guillermo Marco Puche</title>
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<p> <span style="font-size:12px;">Guillermo Marco Puche<br>
Bioinformatician, Computer Science Engineer.<br>
Sistemas Genómicos S.L.<br>
Phone: +34 902 364 669 (Ext.777)<br>
Fax: +34 902 364 670<br>
<a href="www.sistemasgenomicos.com" target="_blank">www.sistemasgenomicos.com</a></span><span
style="font-size:11px;"></span></p>
</td>
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<p> <span style="font-size:10px;"><a
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