Template:BamUtilPrograms

BamUtil is built using libStatGen. Running bin/bam with no parameters will print the usage information for the bam executable. Running bin/bam subProgram will print the usage information for the BamUtil sub-program.

Tools to Rewrite SAM/BAM Files:

• convert - Convert SAM/BAM to SAM/BAM (optionally converts between '=' & bases in the sequence
• writeRegion - Write a file with reads in the specified region and/or have the specified read name
• splitChromosome - Split BAM into 1 file per Chromosome
• splitBam - Split BAM into 1 file per Read Group
• findCigars - Output just the reads that contain any of the specified CIGAR operations.
• BAM Recovery - Recover corrupted BAM files

Tools to Modify & write SAM/BAM Files:

• clipOverlap - Clip overlapping read pairs in a SAM/BAM File already sorted by Coordinate or ReadName so they do not overlap
• filter - Filter reads by soft 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 - Reduce file 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 '!' or by doing soft clips
• mergeBam - Merge multiple BAMs and headers appending ReadGroupIDs if necessary
• polishBam - Add/update header lines & add the RG tag to each record
• dedup - Mark or remove duplicates, can also perform recalibration
• recab - Recalibrate base qualities

Informational Tools:

• validate - Validate a SAM/BAM File, checking file format & printing statistics
• diff - Diff 2 coordinate sorted SAM/BAM files.
• stats - Generate some basic statistics for a SAM/BAM file
• gapInfo - Print information on the gap between read pairs in a SAM/BAM File.

Helper Tools to Print Information In Readable Format:

• dumpHeader - Print the SAM/BAM Header to the screen
• dumpRefInfo - Print SAM/BAM Reference Name Information from the header
• dumpIndex - Print BAM Index File to the screen in a readable format
• readReference - Print the reference string for the specified region to the screen
• explainFlags - Describe SAM/BAM flags

Additional Tools:

• bam2FastQ - Convert the specified BAM file to fastQs.

Dummy/Example Tools:

• readIndexedBam - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file

ASP programs: ASP is a new format that is currently in production, so this tool is not yet available for public release.

• asp - perform an asynchronous pileup producing an ASP file.
• dumpAsp - perform an asynchronous pileup producing an ASP file.