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BamUtil: polishBam

Revision as of 13:46, 29 October 2010 by Mktrost (talk | contribs)

Contents

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>