sam-add-tag-from-fastq: adds a tag to each SAM record with the corresponding sequence from a FASTQ file.

sam-count-secondary: counts and adds a tag with the number of alignments for each read.

sam-mark-dups: finds SAM records with the same start and end position and marks them as duplicates.

sam-per-ref-count: count number of reads aligned on each reference sequence.

sam-tag-to-fasta: extract a SAM tag for each record and print it in FASTA format (useful for tags with sequences).

sam-tag-value-dist: measures how many times each tag value is found in SAM file.

sam-to-bed: converts a SAM file to BED.

sam-to-bedgraph: converts a SAM file to BEDGRAPH.

sam-to-bigwig: converts a SAM file to BIGWIG.

sam-to-collapsed: finds SAM records with the same start and end position and keeps only one.