HISAT-genotype using custom variants

[igordot]

I just found out about HISAT-genotype. After checking the documentation for hisatgenotype_build_genome.py, it seems that a genotype genome can only be created for GRCh38 and for specific databases. Is it possible to create genotype genomes based on other non-human reference genomes and/or based on custom set of variants?

[chbe-helix]

Hi igordot,

It should be possible to generate a custom genotype genome with your own variants for your organism of interest with the current tools. We are currently working on updating the documentation and streamlining the process. Feel free to contact us with more specifics about what you're trying to build and we can help you through the process.

Thanks!

[igordot]

Do you have an estimated timeline?

I am primarily interested in DNA fingerprinting.

[chbe-helix]

The documentation should be completed in less than a month. The streamlining process is currently estimated to be 3 months. I will be sure to include documentation on building DNA fingerprinting loci.

[chbe-helix]

Hi igordot,

I wanted to check in with you and let you know we have transitioned to a new website and HISATgenotype version where we are placing tutorials: https://daehwankimlab.github.io/hisat-genotype/

I'm sorry it is taking so long to get to the DNA fingerprinting tutorial. If you are still interested in getting it working for other species, I'd like to have an off-line conversation with you to discuss your needs and see if I can get a tutorial built to your situation.

Thanks! I look forward to hearing from you!

[igordot]

Thank you for following up. I am excited to hear there is progress.

What would be a good way to contact you? Should I use the email on your profile?

[chbe-helix]

Yes, you can use that email address.