agat_convert_sp_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_sp_minimap2_bam2gff.pl -i infile.bam [ -o outfile ]
agat_convert_sp_minimap2_bam2gff.pl -i infile.sam [ -o outfile ]
agat_convert_sp_minimap2_bam2gff.pl --help
OPTIONS¶
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.
-h or --help
Display this helpful text.