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BamUtil: polishBam

379 bytes added, 13:46, 29 October 2010
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== Trim Polish BAM ==The <code>trimBampolishBam</code> program is released as part of the StatGen Library & Tools download.
<code>trimBampolishBam</code> trims the end of reads in a SAM/BAM file, changing read ends to ‘N’ and quality to ‘!’.
=== Parameters ===
Required Parametersparameters: inFile -i/--in : the SAMinput BAM file -o/--out : output BAM file to Optional parameters: -v : turn on verbose mode -l/--log : writes logfile. <outBamFile>.log will be readused if value is unspecified outFile --HD : the SAMadd @HD header line --RG : add @RG header line --PG : add @PG header line -f/BAM --fasta : fasta reference file to be writtencompute MD5sums and update SQ tags --AS : AS tag for genome assembly identifier num-bases-toUR : UR tag for @SQ tag (if different from --fasta) -trim-onSP : SP tag for @SQ tag -each-side checkSQ : check the number consistency of bases/qualities to trim from each sideSQ tags (SN and LN) with existing header lines. Must be used with --fasta option
=== Example Output ===
Arguments polishBAM (options) --in effect: Input file : testFiles/testSam.sam Output file : results/trimSam.sam #TrimBases : 2 Number of records read = 10Number of records written <inBamFile> --out= 10<outBamFile>

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