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*[[QPLOT]] - Calculate & plot summary statistics
*[[QPLOT]] - Calculate & plot summary statistics
*[[BamUtil: validate|Validate]] – Check file format & print statistics
*[[BamUtil: validate|Validate]] – Check file format & print statistics
*[[VerifyBamID]] – Check sample identities for contamination/sample swap
**Genotype concordance based detection
**Estimate based on population allele frequencies without genotype data
*[[BamUtil: diff|Diff]] - Print the diffs between 2 bams
*[[BamUtil: stats|Stats]] - Print the diffs between 2 bams
==== Rewrite SAM/BAM file ====
*[[BamUtil: convert|Convert]] – Convert between SAM & BAM
*[[BamUtil: convert|Convert]] – Convert between SAM & BAM
*[[BamUtil: writeRegion|WriteRegion]] – Write only reads in the specified region
*[[SplitBam]] – Split into 1 file per Read Group
*[[BamUtil: splitChromosome|SplitChromosome]] – Split into 1 file per Chromosome
*[[BamUtil: writeRegion|WriteRegion]] – Write only reads in the specified region and/or have the specified read name
*[[Pileup]] – Pileup every base or just bases in specified region and write VCF
*[[Pileup]] – Pileup every base or just bases in specified region and write VCF
*[[BamUtil: readIndexedBam|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
*[[BamUtil: readIndexedBam|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
*[[TrimBam]] – Trim end of reads, changing read ends to ‘N’ & quality to ‘!’
*[[TrimBam]] – Trim end of reads, changing read ends to ‘N’ & quality to ‘!’
*[[BamUtil: filter|Filter]] – Soft clip ends with too high mismatch % and mark unmapped if quality of mismatches is too high
*[[BamUtil: filter|Filter]] – Soft clip ends with too high mismatch % and mark unmapped if quality of mismatches is too high
*[[BamUtil: revert|Revert]] - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags
*[[BamUtil: squeeze|Squeeze]] - Reduce 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
*[[SplitBam]] – Split into 1 file per Read Group
*[[BamUtil: splitChromosome|SplitChromosome]] – Split into 1 file per Chromosome
==== Helper Tools to Print Readable Information ====
==== Helper Tools to Print Readable Information ====
