Contributers: Harriet Dashnow, Michael Goldberg, Brent Pedersen
inSTRbility: STR instability
Takes aligned cram input. Extracts the portions of reads that overlap a given locus. Writes these as a fasta file. These will be used to measure the degree of STR instability at a given locus. This is being developed with ONT data.
Usage:
python extract-region.py --out sample.fasta sample.cram