- Convert a sorted BAM file into ALR format - bam2alr -r $reference $bamfile > $Bam2alr_outfile sam2alr This wrapper can be used to launch bam2alr on a sorted and indexed bam file. This can be done either using the Galaxy wrapper sam2bam or this command line : samtools view -@ 8 -uhSt ref.fasta test.sam | samtools sort -@ 8 - test samtools index test.bam -------- **Generated By Khalid BELKHIR**: