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