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.