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Is it possible to run VEP on a merged VCF file derived from a 30 VCFs from the separate reference gene alignments?

Is it possible to run VEP on a merged VCF file derived from a 30 VCFs from the separate reference gene alignments? And is there any rational way to run VEP on a batch of separate VCFs?

annotation vep vcf human
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updated by Emily Emily • written by mathisdead • mathisdead

Better title: Running VEP on VCF with samples aligned to separate reference genomes (.... What?)

How did you merge VCFs with samples aligned to different ref genomes? Any proper merge operation would need exactly one ref genome to perform the merge.

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written by Ram Ram

Hello mathisdead!

We believe that this post does not fit the main topic of this site.

Not a real question (bot)

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

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written by Michael Dondrup Michael Dondrup

1 answer

VCF format should not allow you to have different reference genomes. You should retain your 30 different files if they use different references.

Running the VEP is simply a case of running a command on the command line. If you want to run it 30 times and you don't feel like writing our the command over and over, you can just use your favourite scripting language to write a short script that runs through your list and plugs the appropriate values into the standard VEP command.

Edit: added highlighting to the text to make it clear what the OP needs to to next.

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written by Emily Emily

thx, show a Python or Ruby code of such a script, pls

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written by mathisdead • mathisdead

Did you try writing a script? Give us an idea of the effort you put in and we'll help you get better at scripting.

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written by Ram Ram

Also, don't forget to follow up on your previous threads.

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. Upvote|Bookmark|Accept

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written by Ram Ram

I've added highlighting to my post to make it clear what you need to do. If you would like help troubleshooting your script, please post it here and we will be willing to help you.

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written by Emily Emily

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