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