BamUtil: polishBam
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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>