The script converts output from minimap2 (bam or sam) into gff file. To get bam from minimap2 use the following command: minimap2 -ax splice:hq genome.fa Asecodes_parviclava.nucest.fa | samtools sort -O BAM -o output.bam To use bam with this script you will need samtools in your path.

SYNOPSIS -i infile.bam [ -o outfile ] -i infile.sam [ -o outfile ] --help


if ( !GetOptions( 'i|input=s' => \$opt_in,

  • -i or --input

    Input file in sam (.sam extension) or bam (.bam extension) format.

  • -b or --bam

    To force to use the input file as sam file.

  • -s or --sam

    To force to use the input file as sam file.

  • -o, --out or --output

    Output GFF file. If no output file is specified, the output will be written to STDOUT.

  • -c or --config

    String - Input agat config file. By default AGAT takes as input agat_config.yaml file from the working directory if any, otherwise it takes the orignal agat_config.yaml shipped with AGAT. To get the agat_config.yaml locally type: "agat config --expose". The --config option gives you the possibility to use your own AGAT config file (located elsewhere or named differently).

  • -h or --help

    Display this helpful text.