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The <code>convert</code> option on the [[bamUtil]] executable reads a SAM/BAM file and writes it as a SAM/BAM file.
The <code>convert</code> option on the [[bamUtil]] executable reads a SAM/BAM file and writes it as a SAM/BAM file.
The executable converts the input file into the format of the output file. So if you want to convert a BAM file to a SAM file, just call:
The executable converts the input file into the format of the output file.
It has options to allow for the conversion of the sequence to/from '=' from/to the actual bases by using the reference sequence.
If you want to convert a BAM file to a SAM file, just call:
<pathToExe>/bam --in <bamFile>.bam --out <newSamFile>.sam
<pathToExe>/bam --in <bamFile>.bam --out <newSamFile>.sam
Don't forget to put in the paths to the executable and your test files.
Don't forget to put in the paths to the executable and your test files.
