Uploaded image for project: 'IGB'
  1. IGB
  2. IGBF-1469

Investigate supporting CRAM files

        Details

        • Story Points:
          3
        • Epic Link:
        • Sprint:
          Winter 2018 Sprint 3, Summer 2019 Sprint 8, Fall 2 2023 Sep 17, Fall 4 2023 Oct 16

          Description

          Discussion on twitter:

          https://twitter.com/pjacock/status/500208907651153920

          CRAM is a compressed, random-access file format used instead of BAM. It may be better. Not yet widely used but may be in future. Supporting CRAM could benefit users.

            Attachments

              Issue Links

              is blocked by

              Task - A task that needs to be done. IGBF-3464 Deploy htsjdk-igb

              • Major - Major loss of function.
              • Closed

                Activity

                Ascending order - Click to sort in descending order
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Probably this is a low-ish priority as CRAM doesn't seem to be gaining much traction. Other things are probably a lot higher priority.

                Show
                ann.loraine Ann Loraine added a comment - Probably this is a low-ish priority as CRAM doesn't seem to be gaining much traction. Other things are probably a lot higher priority.
                Hide
                Permalink
                nfreese Nowlan Freese added a comment -

                The Genome in a Bottle project has ultralong Oxford Nanopore alignments in cram format.

                Show
                nfreese Nowlan Freese added a comment - The Genome in a Bottle project has ultralong Oxford Nanopore alignments in cram format.
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Task:

                • Investigate and understand the format - make notes here
                • Investigate tooling in htsjdk library to determine if parsing code is available there
                Show
                ann.loraine Ann Loraine added a comment - Task: Investigate and understand the format - make notes here Investigate tooling in htsjdk library to determine if parsing code is available there
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Blog post about CRAM - https://brentp.github.io/post/cram-speed/

                Show
                ann.loraine Ann Loraine added a comment - Blog post about CRAM - https://brentp.github.io/post/cram-speed/
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Also see: https://www.ga4gh.org/news/cram4gh-twitter-chat-recap/

                Show
                ann.loraine Ann Loraine added a comment - Also see: https://www.ga4gh.org/news/cram4gh-twitter-chat-recap/
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Nowlan Freese : Consumer genomics companies are using CRAM to distribute data to customers.
                [~aloraine] : Situation has changed. We now have even better reasons to support CRAM natively.

                Show
                ann.loraine Ann Loraine added a comment - Nowlan Freese : Consumer genomics companies are using CRAM to distribute data to customers. [~aloraine] : Situation has changed. We now have even better reasons to support CRAM natively.
                Hide
                Permalink
                nfreese Nowlan Freese added a comment - - edited

                I have attached example files for bam (and bai index), sam, and cram (and crai index). Files were created from the same original bam file using samtools - http://lorainelab-quickload.scidas.org/rnaseq/A_thaliana_Jun_2009/auxin_arf19/Col.C.bam. File contains RNA-Seq data from Arabidopsis thaliana (A_thaliana_Jun_2009) within Chr1:6,689-8,835

                Show
                nfreese Nowlan Freese added a comment - - edited I have attached example files for bam (and bai index), sam, and cram (and crai index). Files were created from the same original bam file using samtools - http://lorainelab-quickload.scidas.org/rnaseq/A_thaliana_Jun_2009/auxin_arf19/Col.C.bam . File contains RNA-Seq data from Arabidopsis thaliana (A_thaliana_Jun_2009) within Chr1:6,689-8,835
                Hide
                Permalink
                kgopu Kaushik Gopu added a comment - - edited

                Blogs I am referring to understand various mapped sequence data formats and their differences:

                Show
                kgopu Kaushik Gopu added a comment - - edited Blogs I am referring to understand various mapped sequence data formats and their differences: https://gatk.broadinstitute.org/hc/en-us/articles/360035890791-SAM-or-BAM-or-CRAM-Mapped-sequence-data-formats#:~:text=SAM%20stands%20for%20Sequence%20Alignment,up%20to%20very%20much%20indeed ).
                Hide
                Permalink
                ann.loraine Ann Loraine added a comment -

                Conclusion: Decided to proceed with supporting CRAM in IGB

                Show
                ann.loraine Ann Loraine added a comment - Conclusion: Decided to proceed with supporting CRAM in IGB

                  People

                  • Assignee:
                    kgopu Kaushik Gopu
                    Reporter:
                    ann.loraine Ann Loraine
                  • Votes:
                    0 Vote for this issue
                    Watchers:
                    3 Start watching this issue

                    Dates

                    • Created:
                      Updated:
                      Resolved: