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== Trim BAM ==
== Polish BAM ==
The <code>trimBam</code> program is released as part of the StatGen Library & Tools download.
The <code>polishBam</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, changing read ends to ‘N’ and quality to ‘!’.
<code>polishBam</code> trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’.
=== Parameters ===
=== Parameters ===
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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
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=== Example Output ===
=== Example Output ===
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polishBAM (options) --in=<inBamFile> --out=<outBamFile>
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