Genotyping STRs in linked-read data

This repository contains Python scripts developed to:

• extract in-repeat repeats (IRRs) using barcodes from linked-read alignments (IRR extraction)
• estimate sizes of genomic intervals by calculating Jaccard index (JI) of barcode sharing (distance estimate)

Dependancies

• NumPy
• Pandas
• pybedtools
• pysam
• TRF (for IRR extraction)
• blastn (for IRR extraction)

Author: Readman Chiu

©️ Canada's Michael Smith Genome Sciences Centre, BC Cancer