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  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

            1. A_thaliana_Jun_2009_Chr1.bam
              143 kB
              Nowlan Freese
            2. A_thaliana_Jun_2009_Chr1.bam.bai
              0.1 kB
              Nowlan Freese
            3. A_thaliana_Jun_2009_Chr1.cram
              78 kB
              Nowlan Freese
            4. A_thaliana_Jun_2009_Chr1.cram.crai
              0.0 kB
              Nowlan Freese
            5. A_thaliana_Jun_2009_Chr1.sam
              803 kB
              Nowlan Freese

              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

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                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.
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                nfreese Nowlan Freese added a comment -

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

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

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

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

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

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

                Conclusion: Decided to proceed with supporting CRAM in IGB

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                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:
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                    Dates

                    • Created:
                      Updated:
                      Resolved: