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Insert mutations in a reference genome from a vcf

Hi Biostars,

I am looking for a tool to introduce variants in a reference genome.

The ideal tool I am looking for:

Takes as input:

  • genome fasta

  • a vcf file

What it does:

  • Insert some of the variants (randomly) present in the vcf into the reference genome

What is the output

  • The ideal output would be a mutated new reference fasta, and a vcf file (The vcf file is not that important).

The reason I am looking for this is because I am working on simulation tool, but I would be happy to rely on a third party software to introduce the mutations.

cheers,

sequencing snp simulation
• 3,951 views • link
updated by WouterDeCoster WouterDeCoster • written by IP IP

2 answers

Not exactly what you are asking but if you are not wedded to specific vcf files then you could go the other way by using mutate.sh from BBMap suite. Lots of processing parameters you can control.

$ mutate.sh

Written by Brian Bushnell
Last modified December 13, 2018

Description:  Creates a mutant version of a genome.

Usage:  mutate.sh in=<input file> out=<output file> id=<identity>
I/O parameters:
in=<file>       Input genome.
out=<file>      Output mutant genome.
vcf=<file>      VCF file showing variants added.
• 0 views • link
written by GenoMax GenoMax

I have test this tool, and it is doing (ultrafastly!) what I was looking for. Thanks!

• 0 views • link
written by IP IP

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

• 0 views • link
written by WouterDeCoster WouterDeCoster

done! it was posted as an comment, so I could not accept it :)

• 0 views • link
written by IP IP

GATK FastaAlternateReferenceMaker does almost what you want, selecting randomly some variants is something you'll have to handle.

• 0 views • link
written by WouterDeCoster WouterDeCoster

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