<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 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>
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<br></blockquote></div><br></div>