pip install https://github.com/AndersenLab/bam-toolbox/archive/0.0.3.tar.gz
bam-toolbox 0.1
usage:
bam <command> [<args>...]
bam -h | --help
bam --version
commands:
coverage
Calculate depth of coverage! There are several ways to do so:
-
Calculate coverage for the whole genome, nuclear genome, and individual chromosomes. Also calculated the mtDNA:nuclear ratio which acts as a proxy for mitochondrial content.
usage:
bam coverage <bam> [options] [--mtchr=<mtchr>]
bam coverage <bam> [options] <chrom:start-end>...
bam coverage <bam> [options] --window=<size>
bam coverage <bam> [options] --regions=<gff/bed>
--header- Output the header line.--mtchr- Specifying a mitochondrial chromosome will output the mtDNA:nuclear DNA ratio, offering an estimate of mitochondrial content.--window- Calculate depth of coverage for given windows across the genome.--regions- Specify a bed or gff file and calculate coverage in those regions.
bam coverage test.bam --tsv --header
Result:
Output is in --tsv format.
ENTITY chrom start end ATTR VALUE DATE
CB4853 I 1 15072434 bases_mapped 1688210 2015-11-08 23:22:39.498133
CB4853 I 1 15072434 depth_of_coverage 0.112006461597 2015-11-08 23:22:39.498242
CB4853 I 1 15072434 breadth_of_coverage 0.0918075342045 2015-11-08 23:22:39.498328
CB4853 I 1 15072434 length 15072434 2015-11-08 23:22:39.498372
CB4853 I 1 15072434 pos_mapped 1383763 2015-11-08 23:22:39.498413
CB4853 II 1 15279421 bases_mapped 1605336 2015-11-08 23:22:39.923802
CB4853 II 1 15279421 depth_of_coverage 0.105065237747 2015-11-08 23:22:39.923880
...
CB4853 mt_nuclear_ratio 51.7503772943 2015-11-08 23:22:41.949819
Formatted Result:
| ENTITY | chrom | start | end | ATTR | VALUE | DATE |
|---|---|---|---|---|---|---|
| CB4853 | I | 1 | 15072434 | bases_mapped | 1.68821e+06 | 2015-11-08 23:26:41.891988 |
| CB4853 | I | 1 | 15072434 | depth_of_coverage | 0.112006 | 2015-11-08 23:26:41.892087 |
| CB4853 | I | 1 | 15072434 | breadth_of_coverage | 0.0918075 | 2015-11-08 23:26:41.892155 |
| CB4853 | I | 1 | 15072434 | length | 1.50724e+07 | 2015-11-08 23:26:41.892198 |
| CB4853 | I | 1 | 15072434 | pos_mapped | 1.38376e+06 | 2015-11-08 23:26:41.892239 |
| CB4853 | II | 1 | 15279421 | bases_mapped | 1.60534e+06 | 2015-11-08 23:26:42.319937 |