BamUtil: polishBam
From Genome Analysis Wiki
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>
