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Dear Will,<br>
<br>
Your explanation is very helpful. I'll try to fix my problems
changing variant order as you mentioned.<br>
Anyways I think for the most part of users, the order should be
chr1-22,X,Y,M (almost all the human references are already sorted
into that order).<br>
<br>
Thank you very much.<br>
<br>
Best regards,<br>
Guillermo.<br>
<br>
<div class="moz-cite-prefix">On 04/30/2014 10:18 AM, Will McLaren
wrote:<br>
</div>
<blockquote
cite="mid:CAMVEDX2pkwcwbDjXrdPOz9xMuZLJcWV4g5LdTvMrLe_iFY7ADQ@mail.gmail.com"
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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