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=== SAM/BAM ===
=== SAM/BAM ===
*[[QPLOT]] - Calculate & plot summary statistics
*[[QPLOT]] - Calculate & plot summary statistics
*[[VerifyBamID]] – Check sample identities for contamination/sample swap
*[[VerifyBamID]] – Check sample identities for contamination/sample swap
**Genotype concordance based detection
**Genotype concordance based detection
**Estimate based on population allele frequencies without genotype data
**Estimate based on population allele frequencies without genotype data
*[[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
*[[SuperDeDuper]] - Determine duplicate alignments, either marking or removing the lower quality duplicates. In addition, it may modify paired-end reads where the ends overlap by soft clipping the end with the lower quality bases in the region of overlap.
*[[SuperDeDuper]] - Determine duplicate alignments, either marking or removing the lower quality duplicates. In addition, it may modify paired-end reads where the ends overlap by soft clipping the end with the lower quality bases in the region of overlap.
*[[RGMergeBam]] – Merge sorted BAM files adding Read Groups
*[[RGMergeBam]] – Merge sorted BAM files adding Read Groups
*[[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 ‘!’
The following tools are part of the [[BamUtil|BamUtil program]].
==== Helper Tools to Print Readable Information ====
==== BAM Util Tools ====
*[[BamUtil: dumpHeader|DumpHeader]] - Print the File Header to the screen.
'''QC/Stats'''
*[[BamUtil: dumpRefInfo|DumpRefInfo]] - Print the reference information from the SAM/BAM header.
*[[BamUtil: validate|validate]] – Check file format & print statistics
*[[BamUtil: dumpIndex|DumpIndex]] - Print the BAM Index to the screen in a readable format
*[[BamUtil: diff|diff]] - Print the diffs between 2 bams
*[[BamUtil: readReference|ReadReference]] - Print the reference string for the specified region to the screen.
*[[BamUtil: stats|stats]] - Generate some statistics for a SAM/BAM file
*[[BamUtil: dumpAsp|DumpAsp]] - perform an asynchronous pileup producing an ASP file. <span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>
'''Rewrite SAM/BAM file'''
*[[BamUtil: convert|convert]] – Convert between SAM & BAM
*[[BamUtil: splitBam|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
*[[BamUtil: convert#BAM File Recovery | BAM Recovery]] - Recover corrupted BAM files
*[[BamUtil: asp | asp]] - perform an asynchronous pileup producing an ASP file. <span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>
'''File Updates'''
*[[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
*[[BamUtil: clipOverlap|clipOverlap]] - Clip overlapping read pairs so they do not overlap
'''Helper Tools to Print Readable Information'''
*[[BamUtil: dumpHeader|dumpHeader]] - Print the File Header to the screen.
*[[BamUtil: dumpRefInfo|dumpRefInfo]] - Print the reference information from the SAM/BAM header.
*[[BamUtil: dumpIndex|dumpIndex]] - Print the BAM Index to the screen in a readable format
*[[BamUtil: readReference|readReference]] - Print the reference string for the specified region to the screen.
*[[BamUtil: dumpAsp|dumpAsp]] - perform an asynchronous pileup producing an ASP file. <span style="color:#D2691E">ASP is a new format that is currently in production, so this tool is not yet available for public release.</span>
