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 ‘!’.


   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


polishBAM (options) --in <inBamFile> --out <outBamFile>

Return Value

Returns 0.

Example Output