agat_convert_minimap2_bam2gff.pl

DESCRIPTION

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

agat_convert_minimap2_bam2gff.pl -i infile.bam [ -o outfile ]
agat_convert_minimap2_bam2gff.pl -i infile.sam [ -o outfile ]
agat_convert_minimap2_bam2gff.pl --help

OPTIONS

• -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.