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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>
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