Question: Hadoop Bam with .bam files
gravatar for shalini.ravishankar
4.6 years ago by
United States
shalini.ravishankar10 wrote:


I am started learning Hadoop Bam. But couldn't figure out the steps how to to split the bam file. 

For example,

I have a file called Example.bam. I loaded the file into hdfs : 

hadoop  fs -put Example.bam ./

When I tried :

hadoop jar /usr/local/hadoop-bam/hadoop-bam-7.0.0-jar-with-dependencies.jar

I got :

Command: cat          concatenation of partial SAM and BAM files
         fixmate      BAM and SAM mate information fixing
         index        BAM indexing
         sort         BAM and SAM sorting and merging
         summarize    summarize SAM or BAM for zooming
         summarysort  sort summary file for zooming
         vcf-sort     VCF and BCF sorting
         view         SAM and BAM viewing

But I couldn't figure out how exactly I need to give index / view to split the .bam file chromosome wise.

It would be really helpful someone provides me with any useful reference. 


hdfs bam hadoop genome • 1.8k views
ADD COMMENTlink modified 4.6 years ago by RamRS23k • written 4.6 years ago by shalini.ravishankar10
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