danbing-tk predict user manual

[JosephLalli]

Hi there,

Thank you for this excellent tool. I'm trying to use it to genotype VNTRs in a diverse panel of WGS samples. I am able to use danbing-tk to align my reads to the 35 genome RPGG reference that you provide.

However, I am really struggling to use the bash script and python script provided to convert these kmer counts into coverage estimates. Even a tool to simply convert kmer counts into uncorrected depth estimates would be handy. I have tried performing this procedure with the test files provided, and the script is currently erroring out while loading the LSB.tsv file into memory. Could you provide a test dataset and test commands to get coverage estimates?

Thank you,
Joe

[JosephLalli]

Putting the problem another way, I'd like to replicate your work in https://www.biorxiv.org/content/10.1101/2022.07.09.499321v1.full. Once I have gam files produced by vg giraffe, how do I use your VNTR region bed files and/or danbing-tk to get estimates of VNTR length?

[joyeuxnoel8]

Hi Joseph,

Thanks for posting the question. We're working on creating a new repo to release scripts used in the HPRC paper. I will point you to the repo once it's there.

-Tony