This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Bam splitting index .sbi ?

Hello all,

I used MarkduplicatesSpark and at the end i obtained a bam splitting index (.sbi). I search on internet but i don't really found what it is exactly and if it's really mandatory ?

Thanks in advance 😀

alignment index gatk
• 1,881 views • link
updated by Pierre Lindenbaum Pierre Lindenbaum • written by quentin54520 • quentin54520

1 answer

https://github.com/samtools/htsjdk/blob/master/src/main/java/htsjdk/samtools/SBIIndex.java

SBI is an index into BGZF-compressed data files, which has an entry for the file position of the start of every nth record.

it allows to split the job in n-parts for Spark

• 0 views • link
written by Pierre Lindenbaum Pierre Lindenbaum

Thanks, but it's really mandatory? I mean if i use the option --create-output-bam-splitting-index=false

it's change something ?

• 0 views • link
written by quentin54520 • quentin54520

Log in to answer this question.

More posts like this