Difference between revisions of "BamUtil: polishBam"
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| − | == | + | == Polish BAM == |
| − | The <code> | + | The <code>polishBam</code> program is released as part of the StatGen Library & Tools download. |
| − | <code> | + | <code>polishBam</code> trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’. |
=== Parameters === | === Parameters === | ||
<pre> | <pre> | ||
| − | + | Required parameters: | |
| − | + | -i/--in : input BAM file | |
| − | + | -o/--out : output BAM file | |
| − | + | Optional parameters: | |
| + | -v : turn on verbose mode | ||
| + | -l/--log : writes logfile. <outBamFile>.log will be used if value is unspecified | ||
| + | --HD : add @HD header line | ||
| + | --RG : add @RG header line | ||
| + | --PG : add @PG header line | ||
| + | -f/--fasta : fasta reference file to compute MD5sums and update SQ tags | ||
| + | --AS : AS tag for genome assembly identifier | ||
| + | --UR : UR tag for @SQ tag (if different from --fasta) | ||
| + | --SP : SP tag for @SQ tag | ||
| + | --checkSQ : check the consistency of SQ tags (SN and LN) with existing header lines. Must be used with --fasta option | ||
</pre> | </pre> | ||
| Line 22: | Line 32: | ||
=== Example Output === | === Example Output === | ||
<pre> | <pre> | ||
| − | + | polishBAM (options) --in=<inBamFile> --out=<outBamFile> | |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
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</pre> | </pre> | ||
Revision as of 14:46, 29 October 2010
Polish BAM
The polishBam program is released as part of the StatGen Library & Tools download.
polishBam trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’.
Parameters
Required parameters:
-i/--in : input BAM file
-o/--out : output BAM file
Optional parameters:
-v : turn on verbose mode
-l/--log : writes logfile. <outBamFile>.log will be used if value is unspecified
--HD : add @HD header line
--RG : add @RG header line
--PG : add @PG header line
-f/--fasta : fasta reference file to compute MD5sums and update SQ tags
--AS : AS tag for genome assembly identifier
--UR : UR tag for @SQ tag (if different from --fasta)
--SP : SP tag for @SQ tag
--checkSQ : check the consistency of SQ tags (SN and LN) with existing header lines. Must be used with --fasta option
Usage
trimBam [inFile] [outFile] [num-bases-to-trim-on-each-side]
Return Value
Returns the SamStatus for the reads/writes. 0 on success.
Example Output
polishBAM (options) --in=<inBamFile> --out=<outBamFile>
