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300 bytes added, 15:21, 30 June 2010
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== Read convert ==The <code>convert</code> option on the bam executable reads a SAM/BAM file and write writes it as a SAM/BAM file ==. This executable takes 2/3 arguments. The first argument is the input file. The second argument is the output file. The executable converts the first input file into the format of the second output file. So if you want to convert a BAM file to a SAM file, from the pipeline/bam/ directory you just call: ./bam --in <bamFile>.bam --out <newSamFile>.sam
Don't forget to put in the paths to the executable and your test files.
The third argument, === Parameters ===<codepre>NOEOF< Required Parameters: --in : the SAM/code>, specifies that BAM file to be read --out : the EndSAM/BAM file to be written Optional Parameters: -Of-File Block should noeof : do not be checked for when opening the expect an EOF block on a bam file.</pre>
=== Usage ===
./bam convert --in <inputFile> --out <outputFile.sam/bam/ubam (ubam is uncompressed bam)> [NOEOF--noeof]
=== Return Value ===
== Print SAM/BAM headerdumpHeader ==The <code>dump_headerdumpHeader</code> option on the bam executable prints the header of the specified SAM/BAM file to cout.
=== Parameters ===
== Split BAM by Chromosome splitChromosome ==
The <code>splitChromosome</code> option on the bam executable splits an indexed BAM file into multiple files based on the Chromosome (Reference Name).
== Dump a dumpIndex ==The <code>dumpIndex</code> option on the bam executable prints BAM index file ==in an easy to read format.
=== Usage ===
./bam dump_index dumpIndex <bamIndexFile>
=== Return Value ===
== Read & Write readIndexedBam ==The <code>readIndexedBam</code> option on the bam executable reads an indexed BAM file ==reference id by reference id -1 to 22 and writes it out as a SAM/BAM file.
=== Usage ===
./bam read_indexed_bam readIndexedBam <inputFilename> <outputFile.sam/bam> <bamIndexFile>
=== Return Value ===
* 0

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