[ensembl-dev] Fwd: Pre-processing VCFs

[Diana Lemos]

Hi Margaret,

Besides following the VCF specification 
https://samtools.github.io/hts-specs/VCFv4.2.pdf, you should make sure 
the VCF file is sorted by chromosome and position - unsorted files slow 
down VEP and use more memory.


Best wishes,

Diana


> Hi –
>
> Beyond using bcftools for splitting multi-allelic sites, what other 
> types of pre-processing do you recommend before the VCF is annotated 
> by VEP?
>
> Best,
>
> Margaret
>
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