Provided by: arden_1.0-4_all
arden-filter - filter a SAM file based on the analysis with ARDEN
arden-filter [INPUT SAM] [OUTPUTFILE] [OPTIONS]...
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.
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