You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
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
The text was updated successfully, but these errors were encountered:
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?
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.
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
The text was updated successfully, but these errors were encountered: