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==== General Tools ====
==== General Tools ====
*[[QPLOT]] - Calculate & plot summary statistics
*[[QPLOT]] - Calculate & plot summary statistics
*[[BamValidator]] – Check file format & print statistics
*[[BamUtil: validator|Validate]] – Check file format & print statistics
*[[C++ Executable: bam#convert|Convert]] – Convert between SAM & BAM
*[[BamUtil: convert|Convert]] – Convert between SAM & BAM
*[[C++ Executable: bam#writeRegion|WriteRegion]] – Write only reads in the specified region
*[[BamUtil: writeRegion|WriteRegion]] – Write only reads in the specified region
*[[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
*[[C++ Executable: bam#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
*[[VerifyBamID]] – Check sample identities for contamination/sample swap
*[[VerifyBamID]] – Check sample identities for contamination/sample swap
**Genotype concordance based detection
**Genotype concordance based detection
*[[PolishBam]] – Add/Update header lines & add RG tag to each record
*[[PolishBam]] – Add/Update header lines & add RG tag to each record
*[[TrimBam]] – Trim end of reads, changing read ends to ‘N’ & quality to ‘!’
*[[TrimBam]] – Trim end of reads, changing read ends to ‘N’ & quality to ‘!’
*[[C++ Executable: bam#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
==== Split the File ====
==== Split the File ====
*[[SplitBam]] – Split into 1 file per Read Group
*[[SplitBam]] – Split into 1 file per Read Group
*[[C++ Executable: bam#splitChromosome|SplitChromosome]] – Split into 1 file per Chromosome
*[[BamUtil: splitChromosome|SplitChromosome]] – Split into 1 file per Chromosome
==== Helper Tools to Print Readable Information ====
==== Helper Tools to Print Readable Information ====
*[[C++ Executable: bam#dumpHeader|DumpHeader]] - Print the File Header to the screen.
*[[BamUtil: dumpHeader|DumpHeader]] - Print the File Header to the screen.
*[[C++ Executable: bam#dumpRefInfo|DumpRefInfo]] - Print the reference information from the SAM/BAM header.
*[[BamUtil: dumpRefInfo|DumpRefInfo]] - Print the reference information from the SAM/BAM header.
*[[C++ Executable: bam#dumpIndex|DumpIndex]] - Print the BAM Index to the screen in a readable format
*[[BamUtil: dumpIndex|DumpIndex]] - Print the BAM Index to the screen in a readable format
*[[C++ Executable: bam#readReference|ReadReference]] - Print the reference string for the specified region to the screen.
*[[BamUtil: readReference|ReadReference]] - Print the reference string for the specified region to the screen.
