poorly built nanopore pipeline. It performs alignment using Minimap2, SV calling using Sniffles and CNVpythor, expansion detection using STRDust, and SNV calling using Clair3. The SNVs are phased using whatshap, and annotated using VEP.
Command line:
python poorpipe.py <ubam_folder> <Sample_ID> <config>
ubam_folder is a folder containing bam files. The config is a json file, the file needs to be edited before running the pipeline.
The pipeline itself requires python 3 and slurmpy.
repeat file
https://harrietdashnow.com/STRchive/data/hg19.STRchive-disease-loci.TRGT.bed