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<p>Hi Margaret, <br>
</p>
<p>Besides following the VCF specification <a
href="https://samtools.github.io/hts-specs/VCFv4.2.pdf">https://samtools.github.io/hts-specs/VCFv4.2.pdf</a>,
you should make sure the VCF file is sorted by chromosome and
position - unsorted files slow down VEP and use more memory. <br>
</p>
<p><br>
</p>
<p>Best wishes,</p>
<p>Diana <br>
</p>
<p><br>
</p>
<blockquote type="cite"
cite="mid:94f4b5b7-e47c-a0d3-676b-557e9e9754f9@ebi.ac.uk">
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<p class="MsoNormal"><span style="font-size:11.0pt">Hi – <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Beyond
using bcftools for splitting multi-allelic sites, what
other types of pre-processing do you recommend before
the VCF is annotated by VEP?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Margaret<o:p></o:p></span></p>
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