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| * Rewrite SAM/BAM Files | | * Rewrite SAM/BAM Files |
| ** [[BamUtil: convert|'''convert''' - Read a SAM/BAM file and write as a SAM/BAM file (optionally converts between '=' & bases in the sequence)]] | | ** [[BamUtil: convert|'''convert''' - Read a SAM/BAM file and write as a SAM/BAM file (optionally converts between '=' & bases in the sequence)]] |
| + | ** [[BamUtil: writeRegion|'''writeRegion''' - Write the alignments in the indexed BAM file that fall into the specified region and/or have the specified read name]] |
| ** [[BamUtil: splitChromosome|'''splitChromosome''' - Split BAM by Chromosome]] | | ** [[BamUtil: splitChromosome|'''splitChromosome''' - Split BAM by Chromosome]] |
− | ** [[BamUtil: writeRegion|'''writeRegion''' - Write the alignments in the indexed BAM file that fall into the specified region and/or have the specified read name]] | + | ** [[BamUtil: splitBam|'''splitBam''' - Split SAM/BAM file by Read Group]] |
| ** [[BamUtil: findCigars|'''findCigars''' - Output just the reads that contain any of the specified CIGAR operations]] | | ** [[BamUtil: findCigars|'''findCigars''' - Output just the reads that contain any of the specified CIGAR operations]] |
− | ** [[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: splitBam|'''splitBam''' - Split SAM/BAM file by Read Group]]
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| | | |
| * Modify & write SAM/BAM Files | | * Modify & write SAM/BAM Files |
| + | ** [[BamUtil: clipOverlap|'''clipOverlap''' - Clip overlapping read pairs so they do not overlap]] |
| ** [[BamUtil: filter|'''filter''' - Filter reads by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high]] | | ** [[BamUtil: filter|'''filter''' - Filter reads by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the 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: revert|'''revert''' - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags]] |
| ** [[BamUtil: squeeze|'''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]] | | ** [[BamUtil: squeeze|'''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]] |
− | ** [[BamUtil: clipOverlap|'''clipOverlap''' - Clip overlapping read pairs so they do not overlap]]
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| | | |
| * Informational Tools | | * Informational Tools |
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| ** [[BamUtil: diff|'''diff''' - Print the diffs between 2 bams]] | | ** [[BamUtil: diff|'''diff''' - Print the diffs between 2 bams]] |
| ** [[BamUtil: stats|'''stats''' - Print some basic statistics on a SAM/BAM file]] | | ** [[BamUtil: stats|'''stats''' - Print some basic statistics on a SAM/BAM file]] |
| + | ** [[BamUtil: gapInfo|'''gapInfo''' - Print information on the gap between read pairs in a SAM/BAM file]] |
| | | |
| * Print Information in Readable Form: | | * Print Information in Readable Form: |
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| ** [[BamUtil: readReference|'''readReference''' - Print the reference string for the specified region]] | | ** [[BamUtil: readReference|'''readReference''' - Print the reference string for the specified region]] |
| | | |
| + | * Dummy/Example Tools: |
| + | ** [[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]] |
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| This executable is built using [[C++ Library: libStatGen]]. | | This executable is built using [[C++ Library: libStatGen]]. |
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| Just running ./bam will print the Usage information for the bam executable. | | Just running ./bam will print the Usage information for the bam executable. |