Usage: modbamtools [OPTIONS] COMMAND [ARGS]...
A set of tools to manipulate and visualize data from base modification bam
files
Options:
--version Show the version and exit. [default: False]
--help Show this message and exit. [default: False]
Commands:
calcMeth Calculate methylation statistics for regions in a bed file
cluster Calculate clustering statistics for regions in a bed file
plot Plot single-read base modification data
plot
Usage: modbamtools plot [OPTIONS] BAMS...
Plot single-read base modification data
Options:
-r, --region TEXT Region of interest. example: chr21:1-1000
-br, --batch PATH makes html/pdf report for all regions in the bed
file
-g, --gtf PATH makes gene tracks from sorted and tabix gtf files
-b, --bed PATH makes tracks from sorted and tabix bed files. This
will plot each interval as a rectangle (similar to
gtf)
-bw, --bigwig PATH makes a track from bigwig files
-bd, --bedgraph PATH makes a track from bedgraph files
-s, --samples TEXT sample names per each bam input
-tr, --track-titles TEXT titles of tracks provided in order of gtf files,
bed files, bigwig files, bedgraph files
-hp, --hap reads will be grouped according to HP tag in bam
(comma separated)
-st, --strands reads will be grouped by strand in bam
-o, --out PATH output path [required]
-p, --prefix TEXT File name for output [default: modbamviz]
-f, --fmt TEXT format of output file (png, html, svg, pdf)
[default: html]
-u, --can_prob FLOAT probability threshold for canonical bases
[default: 0.5]
-m, --mod_prob FLOAT probability threshold for modified bases
[default: 0.5]
-h, --height INTEGER height of plot in px. This is for fine tuning, the
height is automatically calculated.
-w, --width INTEGER width of plot in px
-c, --cluster cluster the reads based on modification state
--help Show this message and exit.
calcMeth
Usage: modbamtools calcMeth [OPTIONS] BAM
Calculate methylation statistics for regions in a bed file
Options:
-b, --bed PATH bed file of regions
-t, --threads INTEGER number of processes [default: 1]
-a, --min_calls INTEGER filter out reads that have fewer number of modified
base calls in region of interest [default: 5]
-s, --min_cov FLOAT minimum percent coverage of a single read over
region of interest [default: 80]
-hp, --hap add stats for each haplotype separately to the
output
-o, --out PATH output path [required]
--help Show this message and exit.
cluster
Usage: modbamtools cluster [OPTIONS] BAM
Calculate clustering statistics for regions in a bed file
Options:
-b, --bed PATH bed file of regions to cluster
-t, --threads INTEGER number of processes [default: 1]
-o, --out PATH output path [required]
--help Show this message and exit.