Great Python tool(s) for simulating fake/dummy VCF files?
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2.3 years ago
BioBing ▴ 150

Hi all,

I need to generate a large number of simulated VCF files to test (and stress test) a system. For legal reasons, the files need to be fake.

Can any of you recommend a great Python tool for generating dummy VCF files?

Thanks!

SNP python • 1.3k views
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2.3 years ago
gb ★ 2.1k

Maybe it is better to simulate fastq files, and create VCF files yourself. This may give a bit more control.

paired-end reads in BBMap randomreads.sh

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Thanks, that is a good way to approach the task!

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2.3 years ago
GenoMax 125k

Actually another tool from BBMap suite called mutate.sh will introduce mutations in a reference you provide. You get control over mutation creation. The tool will also create a corresponding VCF file for the mutations it creates. See the inline help for more information.

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Great recommendation, thanks!

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