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