Home Software Services About Contact     

sam2aln command

Convert alignments in SAM format to a human-readable, BLAST-like format.

The SAM filename to convert is specified following -sam2aln.

A FASTA filename for the reference genome is specified by the -ref option (required).

The output filename is specified by the -output option. To send output to a pipe, use /dev/stdout as the filename.


urmap -sam2aln reads.sam -ref hg38.fasta -output reads.aln