Hadoop BAM - how to use?

Question

[shalini.ravishankar]

Hello everyone,

Can someone explain me how to use Hadoop BAM. I am new to this field. I would really appreciate the help.

[Pierre Lindenbaum]

just curious: what do you want to achieve with HadoopBam ? (I don't know this hadoop-based tool)

Answer 1

[ppatil]

hello,shalini.ravishankar Hadoop-BAM is a Java library for the manipulation of files in common bioinformatics formats using the Hadoop MapReduce framework with the Picard SAM JDK, and command line tools similar to SAMtools.

You need to import the libraries into a java program, write and compile code that leverages these libraries, and then execute the map-reduce JARs. The BAM files would then sit directly in HDFS and can be put there using the Hadoop filesystem commands.

[lakhujanivijay]

Hi ppatil

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