NAME

coverm filter - Threshold alignments with insufficient identity (version 0.5.0)

SYNOPSIS

coverm filter FLAGS OPTIONS

DESCRIPTION

Only primary, non-supplementary alignments are considered, and output files are grouped by reference, but not sorted by position.

FLAGS

--inverse

Only keep reads which are unmapped or align below thresholds. Note that output records may still be marked as mapped if they do not meet the thresholds. [default: not set]

-v, --verbose

Print extra debugging information. [default: not set]

-q, --quiet

Unless there is an error, do not print log messages. [default: not set]

-h, --help

Output a short usage message. [default: not set]

--full-help

Output a full help message and display in 'man'. [default: not set]

--full-help-roff

Output a full help message in raw ROFF format for conversion to other formats. [default: not set]

OPTIONS

-b, --bam-files PATH ..

Path to reference-sorted BAM file(s). [required]

-o, --output-bam-files PATH ..

Path to corresponding output file(s). [required]

-t, --threads INT

Number of threads for output compression. [default: 1]

ALIGNMENT THRESHOLDING

--min-read-aligned-length INT

Exclude reads with smaller numbers of aligned bases. [default: 0]

--min-read-percent-identity FLOAT

Exclude reads by overall percent identity e.g. 0.95 for 95%. [default: 0.0]

--min-read-aligned-percent FLOAT

Exclude reads by percent aligned bases e.g. 0.95 means 95% of the read's bases must be aligned. [default: 0.0]

--min-read-aligned-length-pair INT

Exclude pairs with smaller numbers of aligned bases. Implies --proper-pairs-only. [default: 0]

--min-read-percent-identity-pair FLOAT

Exclude pairs by overall percent identity e.g. 0.95 for 95%. Implies --proper-pairs-only. [default: 0.0]

--min-read-aligned-percent-pair FLOAT

Exclude reads by percent aligned bases e.g. 0.95 means 95% of the read's bases must be aligned. Implies --proper-pairs-only. [default: 0.0]

--proper-pairs-only

Require reads to be mapped as proper pairs. [default: not set]

--exclude-supplementary

Exclude supplementary alignments. [default: not set]

EXIT STATUS

0

Successful program execution.

1

Unsuccessful program execution.

101

The program panicked.

AUTHOR

Ben J. Woodcroft, Centre for Microbiome Research, Queensland University of Technology <benjwoodcroft near gmail.com>