Two modifications:
The first one is to output some key information in different stages of Straglr, such as informing users how many loci are loaded and will be genotyped or when to construct input of TRF and when to run GMM for genotyping alleles of VNTRs.
The second one is integrating out_prefix to temporary file of TRF.
These codes are modified from this repository.
And citation:
Chiu R, Rajan-Babu IS, Friedman JM, Birol I. Straglr: discovering and genotyping tandem repeat expansions using whole genome long-read sequences. Genome Biol 22, 224 (2021). https://doi.org/10.1186/s13059-021-02447-3