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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. |
| | | |
− | <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> |
| | | |
− | | + | = 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> |
| + | {{PhoneHomeParamDesc}} |
| + | |
| + | == Required Parameters == |
| + | {{InBAMInputFile}} |
| + | {{OutBAMOutputFile}} |
| + | |
| + | == Optional Parameters == |
| + | === Verbose (<code>--verbose</code>) === |
| + | Use <code>--verbose</code> to turn on verbose mode. |
| + | |
| + | === Specify Log Filename (<code>--log</code>) === |
| + | Use <code>--log</code> followed by the log filename to specify the log filename. Default is the output file basename with a <code>.log</code> extension |
| + | |
| + | === Add the HD Header (<code>--HD</code>) === |
| + | Use <code>--HD</code> followed by the HD header line to add a HD header. Be sure to include "@HD" in the line you specify. |
| + | |
| + | === Add the RG Header (<code>--RG</code>) === |
| + | Use <code>--RG</code> followed by the RG header line to add a RG header. Be sure to include "@RG" in the line you specify. |
| + | |
| + | === Add the PG Header (<code>--PG</code>) === |
| + | Use <code>--PG</code> followed by the PG header line to add a PG header. Be sure to include "@PG" in the line you specify. |
| + | |
| + | === Add MD5 and UR tags to SQ Headers (<code>--fasta</code>) === |
| + | Use <code>--fasta</code> followed by the fasta reference file name to compute MD5sums and update SQ tags with the M5 & UR values. Use the [[#Add the UR tag to SQ Headers (--UR)|<code>--UR</code>]] option to specify a different UR value. |
| + | |
| + | === Add the AS tag to SQ Headers (<code>--AS</code>) === |
| + | Use <code>--AS</code> followed by the genome assembly identify to add the AS tag to the SQ Headers. |
| + | |
| + | === Add the UR tag to SQ Headers (<code>--UR</code>) === |
| + | Use <code>--UR</code> followed by the URI of the sequence to add the UR tag to the SQ Headers. |
| | | |
− | === Usage ===
| + | The UR header will be automatically added with the [[#Add MD5 and UR tags to SQ Headers (--fasta)|<code>--fasta</code>]] option, so if [[#Add MD5 and UR tags to SQ Headers (--fasta)|<code>--fasta</code>]] is used, <code>--UR</code> only needs to be specified if it is different from [[#Add MD5 and UR tags to SQ Headers (--fasta)|<code>--fasta</code>]]. |
− | polishBAM (options) --in <inBamFile> --out <outBamFile>
| |
| | | |
| + | === Add the SP tag to SQ Headers (<code>--SP</code>) === |
| + | Use <code>--SP</code> followed by the species to add the SP tag to the SQ Headers. |
| | | |
− | === Return Value ===
| + | {{PhoneHomeParameters}} |
− | Returns 0.
| |
| | | |
− | === Example === | + | = Return Value = |
| + | Returns 0 on success, non-0 on failure. |
| + | |
| + | = 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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| </pre> | | </pre> |
| | | |
| + | |
| + | [[Category:BamUtil|polishBam]] |
| + | [[Category:BAM Software]] |
| [[Category:Software]] | | [[Category:Software]] |
− | [[Category:StatGen Download]]
| |
− | [[Category:BAM Software]]
| |