Suite of command-line tools for manipulating SAM files.

Usage: bam <tool> [<tool arguments>] Just enter 'bam <tool>' to see its usage instructions. E.g. 'bam filter'.

Rewrite SAM/BAM Files

convert - Convert SAM/BAM to SAM/BAM
writeRegion - Write a file with reads in the specified region and/or have the specified read name
splitChromosome - Split BAM by Chromosome
splitBam - Split a BAM file into multiple BAM files based on ReadGroup
findCigars - Output just the reads that contain any of the specified CIGAR operations.

Modify & write SAM/BAM Files

clipOverlap - Clip overlapping read pairs in a SAM/BAM File already sorted by Coordinate or ReadName
filter - Filter reads by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high
revert - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags
squeeze - reduces files size by dropping OQ fields, duplicates, & specified tags, using '=' when a base matches the reference, binning quality scores, and replacing readNames with unique integers
trimBam - Trim the ends of reads in a SAM/BAM file changing read ends to 'N' and quality to '!'
rgMergeBam - merge multiple BAMs and headers appending ReadGroupIDs
polishBam - adds/updates header lines & adds the RG tag to each record
dedup - Mark Duplicates
recab - Recalibrate