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, 14:18, 3 January 2014
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| ==== BAM Util Tools ==== | | ==== BAM Util Tools ==== |
− | The following tools are part of the [[BamUtil|BamUtil program]].
| + | {{BamUtilPrograms}} |
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− | '''QC/Stats'''
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− | *[[BamUtil: validate|validate]] – Check file format & print statistics
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− | *[[BamUtil: diff|diff]] - Print the diffs between 2 bams
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− | *[[BamUtil: stats|stats]] - Generate some statistics for a SAM/BAM file
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− | '''Rewrite SAM/BAM file'''
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− | *[[BamUtil: convert|convert]] – Convert between SAM & BAM
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− | *[[BamUtil: splitBam|splitBam]] – Split into 1 file per Read Group
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− | *[[BamUtil: splitChromosome|splitChromosome]] – Split into 1 file per Chromosome
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− | *[[BamUtil: writeRegion|writeRegion]] – Write only reads in the specified region and/or have the specified read name
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− | *[[BamUtil: convert#BAM File Recovery | BAM Recovery]] - Recover corrupted BAM files
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− | *[[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>
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− | '''File Updates'''
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− | *[[BamUtil: dedup|dedup]] – Mark or remove duplicates, can also perform recalibration
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− | *[[BamUtil: recab|recab]] - Recalibrate base qualities based on an adaptive logistic regression model
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− | *[[BamUtil: clipOverlap|clipOverlap]] - Clip overlapping read pairs so they do not overlap
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− | *[[BamUtil: filter|filter]] – Soft clip ends with too high mismatch % and mark unmapped if quality of mismatches is too high
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− | *[[BamUtil: revert|revert]] - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags
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− | *[[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
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− | *[[BamUtil: trimBam| trimBam]] – Trim end of reads, changing read ends to ‘N’ & quality to ‘!’
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− | *[[BamUtil: polishBam|polishBam]] – Add/Update header lines & add RG tag to each record
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− | *[[BamUtil: rgMergeBam|rgMergeBam]] – Merge sorted BAM files adding Read Groups
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− | '''Additional Tools'''
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− | * [[BamUtil: bam2FastQ|bam2FastQ]] - Convert the specified BAM file to fastQs
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− | '''Helper Tools to Print Readable Information'''
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− | *[[BamUtil: dumpHeader|dumpHeader]] - Print the File Header to the screen.
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− | *[[BamUtil: dumpRefInfo|dumpRefInfo]] - Print the reference information from the SAM/BAM header.
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− | *[[BamUtil: dumpIndex|dumpIndex]] - Print the BAM Index to the screen in a readable format
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− | *[[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>
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− | *[[BamUtil: readReference|readReference]] - Print the reference string for the specified region to the screen.
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| === FASTQ === | | === FASTQ === |