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
- 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
- bam2FastQ - Convert the specified BAM file to fastQs.
- 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.