To randomly generate a list of insertions and deletions

Question

[xmy1990]

Hi, I want to get many random insertions and deletions of specified sizes. For example, 10 insertions with size between 20bp and 30 bp 10 deletions with size between 20bp and 30 bp

How to randomly generate them with chrom, pos, start, end, ref, alt ?

Thanks!

[Istvan Albert]

What is your input and output data?

A genome in FASTA format and you want to end up with another genome as in FASTA format with the mutations?

[xmy1990]

Thanks,

input: hs37d5.fa, sizes of insertions and deletions

output: #CHROM POS ID REF ALT

such as,

chr1    1147985    C       CCAGCCCCTCCCAGCCCCTGGCCCCTCTGCCCCCTCA 
chr1    3319601    ACCCTCCTCTGAGTCTTCCTCCCCTTCCCGTG        A 

Are there any ready-made tools that can do this?

Thanks

Answer 1

[Istvan Albert]

There is a tool called simuG that has many options that seem to include what you are after:

• https://github.com/yjx1217/simuG

[xmy1990]

Thanks,

I have used https://github.com/yjx1217/simuG to do randomly generate a list of insertions and deletions.