Man page - cnvkit-autobin(1)
Packages contains this manual
- cnvkit-import-theta(1)
- cnvkit-coverage(1)
- cnvkit-metrics(1)
- cnvkit-import-seg(1)
- cnvkit-export(1)
- cnvkit-breaks(1)
- cnvkit-fix(1)
- cnvkit-segmetrics(1)
- cnvkit-batch(1)
- cnvkit-import-rna(1)
- cnvkit-bintest(1)
- cnvkit-diagram(1)
- cnvkit-call(1)
- cnvkit-autobin(1)
- cnvkit-access(1)
- cnvkit-antitarget(1)
- cnvkit-sex(1)
- cnvkit-segment(1)
- cnvkit-genemetrics(1)
- cnvkit-heatmap(1)
- cnvkit-target(1)
- cnvkit-import-picard(1)
- cnvkit-reference(1)
- cnvkit-scatter(1)
apt-get install cnvkit
Manual
CNVKIT_AUTOBIN
NAMEDESCRIPTION
positional arguments:
options:
NAME
cnvkit_autobin - Quickly calculate reasonable bin sizes from BAM read counts.
DESCRIPTION
usage: cnvkit.py
autobin [-h] [-f FILENAME] [-m {hybrid,amplicon,wgs}]
[-g FILENAME] [-t TARGETS] [-b BP_PER_BIN]
[--target-max-size BASES] [--target-min-size BASES] [--antitarget-max-size BASES] [--antitarget-min-size BASES] [--annotate FILENAME] [--short-names] [--target-output-bed FILENAME] [--antitarget-output-bed FILENAME] bams [bams ...]
positional arguments:
|
bams |
Sample BAM file(s) to test for target coverage |
options:
-h , --help
show this help message and exit
-f FILENAME, --fasta FILENAME
Reference genome, FASTA format (e.g. UCSC hg19.fa)
-m {hybrid,amplicon,wgs}, --method {hybrid,amplicon,wgs}
Sequencing protocol: hybridization capture (’hybrid’), targeted amplicon sequencing (’amplicon’), or whole genome sequencing (’wgs’). Determines whether and how to use antitarget bins. [Default: hybrid]
-g FILENAME, --access FILENAME
Sequencing-accessible genomic regions, or exons to use as possible targets (e.g. output of refFlat2bed.py)
-t TARGETS, --targets TARGETS
Potentially targeted genomic regions, e.g. all possible exons for the reference genome. Format: BED, interval list, etc.
-b BP_PER_BIN, --bp-per-bin BP_PER_BIN
Desired average number of sequencing read bases mapped to each bin. [Default: 100000.0]
--target-max-size BASES
Maximum size of target bins. [Default: 20000]
--target-min-size BASES
Minimum size of target bins. [Default: 20]
--antitarget-max-size BASES
Maximum size of antitarget bins. [Default: 500000]
--antitarget-min-size BASES
Minimum size of antitarget bins. [Default: 500]
--annotate FILENAME
Use gene models from this file to assign names to the target regions. Format: UCSC refFlat.txt or ensFlat.txt file (preferred), or BED, interval list, GFF, or similar.
--short-names
Reduce multi-accession bait labels to be short and consistent.
--target-output-bed FILENAME
Filename for target BED output. If not specified, constructed from the input file basename.
--antitarget-output-bed FILENAME
Filename for antitarget BED output. If not specified, constructed from the input file basename.