covtobed
covtobed: a simple and fast tool to extract coverage tracks from BAM files - Published in JOSS (2020)
https://github.com/alejandrogzi/bed2gff
cool BED-to-GFF3 converter that runs in parallel
https://github.com/alexpreynolds/soda
Python-based UCSC genome browser snapshot-taker and gallery-maker
https://github.com/alexpreynolds/hglive
HiGlass-backed dynamic BED gallery browser
https://github.com/alejandrogzi/packbed
pack a .bed into overlapping components
https://github.com/alexpreynolds/sample
Performs memory-efficient reservoir sampling on very large input files delimited by newlines
https://github.com/cumbof/tcga2bed
The Cancer Genome Atlas Data Extraction and Conversion Tool
https://github.com/cumbof/opengdc
An open-source Java tool to automatically extract and convert all clinical and genomic data from the Genomic Data Commons to BED, GTF, CSV, and JSON format
https://github.com/alejandrogzi/gxf2bed
fastest GTF/GFF-to-BED converter chilling around
https://github.com/cumbof/opengdc.py
Python implementation of the OpenGDC software https://github.com/cumbof/OpenGDC
https://github.com/alexpreynolds/cull-exemplars
Filter lower-scoring, neighboring genomic intervals within a specified distance