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To randomly generate a list of insertions and deletions

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!

si
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written by xmy1990 • xmy1990

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?

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written by Istvan Albert Istvan Albert

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

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updated by Istvan Albert Istvan Albert • written by xmy1990 • xmy1990

1 answer

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

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written by Istvan Albert Istvan Albert

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