[ensembl-dev] VCF order chrX, chrM

[Guillermo Marco Puche]

Dear developers,

I'm experiencing a strange behavior when annotating a full sorted VCF file.
My chr order is the following: chr1 to chr22, chrX, chrY, chrM.

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:

Imagine I've the following variants in my vcf:

chrX variant1
chrX variant2
chrX variant3
chrX variant4
chrM variant1
chrM variant2

After annotating the VCF the order remains like this:

chrX variant1
chrX variant2
chrM variant1
chrM variant2
chrX variant3
chrX variant4

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.

Thank very much.

Best regards,
Guillermo.
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