Notice:
If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!

Test-drive the GATK tools and Best Practices pipelines on Terra


Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.

Can I use htsjdk Java plugin to return a byte range of a requested chromosome on a .bam/.sam file?

I've read through this documentation: https://samtools.github.io/hts-specs/SAMv1.pdf

From my very rough understanding, the index file requests information from the .bam file by using requesting the bin.

I'm attempting to request a partial file from Google Drive, the only way I can do this is to tell the Drive api a byte range that I want. Is there anything in the htsjdk library that can provide this? Is there any way that I can get a bin number, and somehow get a byte range from that?

Answers

Sign In or Register to comment.