Usage: gataca.py [OPTIONS] <sample.bam> <reference.fasta>

Options:
  -h, --help                          show this help message and exit

  Input/output:
    -r STR, --region=STR              specify region (chr:from-to) of your interest, default: whole genome
    -o STR, --output=STR              name of output VCF file, default: standard output

  Reads:
    -p STR, --policy=STR              set how reads were sequenced (fr, rf) [fr]
    -q INT, --min_quality=INT         minimal mapping Phred quality score of read [30]
    -l INT, --min_length=INT          minimal length of split part [10]

  Depth of coverage:
    -w INT, --window_size=INT         size of window for getting coverage [100]
    -c STR, --coverage=STR            interval (min,max) of accepted coverage in windows, default: estimate from reads
    -a FLOAT, --coverage_core=FLOAT   core of windows from which min and max allowed coverage will be estimated [0.1]
    -u INT, --min_coverage_count=INT  minimal number of windows in core [1000]

  Insert size:
    -i STR, --insert_size=STR         interval (min,max) of accepted size between reads, default: estimate from reads
    -n INT, --insert_reads=INT        number of reads from which insert size will be estimated [50000]
    -e FLOAT, --insert_core=FLOAT     core of reads_num from which min and max insert size will be estimated [0.1]
    -m INT, --min_insert_count=INT    minimal number of reads in core [1000]

  Variations:
    -v FLOAT, --min_confidence=FLOAT   minimal confidence about variation [0.3]