Great Python tool(s) for simulating fake/dummy VCF files?

Question

[BioBing]

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!

Answer 1

[gb]

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

[BioBing]

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

Answer 2

[GenoMax]

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.

[BioBing]

Great recommendation, thanks!