Man page - arden-filter(1)

Packages contains this manual

Package:  arden
apt-get install arden

Manuals in package:
• arden-create(1)
• arden-analyze(1)
• arden-filter(1)
Documentations in package:
• arden

Manual

ARDEN-FILTER

NAME
SYNOPSIS
DESCRIPTION
OPTIONS

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NAME

arden-filter - filter a SAM file based on the analysis with ARDEN

SYNOPSIS

arden-filter [ INPUT SAM ] [ OUTPUTFILE ] [ OPTIONS ]...

DESCRIPTION

Script to filter and a SAM file based on the analysis with ARDEN. It is necessary to specify the desired cutoffs for RQS,GAPS and MM. Type: python filter -e 1 for printing some examples.

OPTIONS

Required Arguments:
OUTPUTFILE

Outputfilename

INPUT

Single SAM file to filter.

--version

show program’s version number and exit

-h , --help

show this help message and exit

-r RQS, --rqs = RQS

Threshold for minimum read quality score.. [default: 0]

-m MM, --mismatches = MM

Threshold for maximum number of mismatches in an alignment [default: 3]

-g GAPS, --gaps = GAPS

Threshold for maximum number of gaps in an alignment. [default: 3]

-e PEXAMPLES, --examples = PEXAMPLES

set to 1 if you want to print examples

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