jmencius/margin repository overview

Margin-v2.3.1 (https://github.com/UCSC-nanopore-cgl/margin/releases/tag/v2.3.1⁠) is licensed under the MIT License (https://github.com/UCSC-nanopore-cgl/margin⁠), which explicitly permits modification, distribution, and redistribution, provided that the original license and copyright notice are retained. In accordance with these terms, I have built a Docker image based on Ubuntu 20.04 to facilitate its use. I am not the author of this software; I have only created the containerized environment for convenience.

The built binary of Margin is at /home/margin-2.3.1/build/margin.

Example:

/home/margin-2.3.1/build/margin phase ./data/HG02723.pacbio.sorted.bam ./ref/GCA_000001405.15_GRCh38_no_alt_analysis_set.fasta ./results/HG02723_pacbio_concated.vcf /home/margin-2.3.1/params/phase/allParams.phase_vcf.pb-hifi.json --threads 48 -o ./results/HG02723_margin --skipHaplotypeBAM -p 49;