cnvkit-autobin1

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.