This is a reimplementation of estMOI in python. Still work in progress.
pip install git+https://github.com/jodyphelan/pyMOI.git
pyMOI --bam <input_bam> --vcf <input_vcf> --outfile <output_json_file>
usage: pyMOI [-h] --bam BAM --vcf VCF --outfile OUTFILE [--maxdist MAXDIST] [--min_count MIN_COUNT]
A simple command line tool for Moi
options:
-h, --help show this help message and exit
--bam BAM BAM (or cram) file
--vcf VCF VCF file
--outfile OUTFILE Name of output file
--maxdist MAXDIST Maximum distance between the first and last SNP
--min_count MIN_COUNT
Minimum count of haplotype