BamUtil: polishBam: Difference between revisions
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Created page with '== Trim BAM == The <code>trimBam</code> program is released as part of the StatGen Library & Tools download. <code>trimBam</code> trims the end of reads in a SAM/BAM file, chang…' |
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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> | |||
</pre> | </pre> | ||
Revision as of 18:46, 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>
