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, 14:47, 3 April 2012
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− | == Polish BAM == | + | = Overview of the <code>polishBam</code> function of <code>bamUtil</code> = |
− | The <code>polishBam</code> program is released as part of the StatGen Library & Tools download. | + | The <code>polishBam</code> option on the [[bamUtil]] executable adds/updates header lines & adds the RG tag to each record. |
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− | <code>polishBam</code> trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’. | + | = Usage = |
| + | ./bam polishBam (options) --in <inBamFile> --out <outBamFile> |
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− | | + | = Parameters = |
− | === Parameters ===
| |
| <pre> | | <pre> |
| Required parameters: | | Required parameters: |
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| --checkSQ : check the consistency of SQ tags (SN and LN) with existing header lines. Must be used with --fasta option | | --checkSQ : check the consistency of SQ tags (SN and LN) with existing header lines. Must be used with --fasta option |
| </pre> | | </pre> |
− |
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− | === Usage ===
| |
− | polishBAM (options) --in <inBamFile> --out <outBamFile>
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− | === Return Value ===
| + | = Return Value = |
| Returns 0. | | Returns 0. |
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− | === Example ===
| + | = Example = |
| Command: | | Command: |
| <pre> | | <pre> |
− | ../../bin/polishBam --in testFiles/sortedSam.sam --out results/updatedSam.sam --log results/updated.log --checkSQ --fasta testFiles/testFasta.fa --AS my37 --UR testFasta.fa --RG "@RG ID:UM0037:1 SM:Sample2 LB:lb2 PU:mypu CN:UMCORE DT:2010-11-01 PL:ILLUMINA" --PG "@PG ID:polish VN:0.0.1" --SP new --HD "@HD VN:1.0 SO:coordinate GO:none"
| + | ./bam polishBam --in testFiles/sortedSam.sam --out results/updatedSam.sam --log results/updated.log --checkSQ --fasta testFiles/testFasta.fa --AS my37 --UR testFasta.fa --RG "@RG ID:UM0037:1 SM:Sample2 LB:lb2 PU:mypu CN:UMCORE DT:2010-11-01 PL:ILLUMINA" --PG "@PG ID:polish VN:0.0.1" --SP new --HD "@HD VN:1.0 SO:coordinate GO:none" |
| </pre> | | </pre> |
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