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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

Checking and comparing SAM/BAM files

  • validate - Validate a SAM/BAM File
  • diff - Diff 2 coordinate sorted SAM/BAM files.
  • stats - Stats a SAM/BAM File
  • gapInfo - Print information on the gap between read pairs in a SAM/BAM File.

Information in readable format

  • dumpHeader - Print SAM/BAM Header
  • dumpRefInfo - Print SAM/BAM Reference Name Information
  • dumpIndex - Print BAM Index File in English
  • readReference - Print the reference string for the specified region

Additional Tools

  • bam2FastQ - Convert the specified BAM file to fastQs.

Dummy/Example Tools

  • readReference - Print the reference string for the specified region