Uploaded image for project: 'User Support'
  1. User Support
  2. HELP-303

VCFv4 compatibility

          Details

          • Story Points:
            2

            Description

            Dear IGB developers,

            I am working with SNP calls, and I cannot get the newest vcf formats to load, which are the standard output from SnpEff. The error I get is "file version not supported VCFv4.2"
            Do you have plans to support VF4, and if not what do you recommend for being able to view my data. Should I just convert back to an earlier version of vcf?
            Thanks
            Alex

            Reporter: Alexander R Leydon
            E-mail: leydon.alexander@gmail.com

              Attachments

                Issue Links

                relates to

                Improvement - An improvement or enhancement to an existing feature or task. IGBF-1380 Support newer VCF - User request

                • Major - Major loss of function.
                • Closed

                  Activity

                  Descending order - Click to sort in ascending order
                  Hide
                  Permalink
                  ieclabau Ivory Blakley (Inactive) added a comment -

                  Ivory sent this message to Alex (the user) on 23 August 2018.
                  _____________________

                  Alex,

                  Thank you for reaching out to the IGB team regarding the VCF v4.2 file format.
                  I am making the modifications to our code base to allow IGB to read the new version of this format.

                  VCF is a very versatile format, so the test file I made cannot represent all of the different styles possible. Are there any VCF files (either v4.2 or v4.3) that you could send or recommend that I could use for testing ?

                  Thank you again for bringing our attention to this issue,

                  Best,
                  Ivory

                  Show
                  ieclabau Ivory Blakley (Inactive) added a comment - Ivory sent this message to Alex (the user) on 23 August 2018. _____________________ Alex, Thank you for reaching out to the IGB team regarding the VCF v4.2 file format. I am making the modifications to our code base to allow IGB to read the new version of this format. VCF is a very versatile format, so the test file I made cannot represent all of the different styles possible. Are there any VCF files (either v4.2 or v4.3) that you could send or recommend that I could use for testing ? Thank you again for bringing our attention to this issue, Best, Ivory
                  Hide
                  Permalink
                  ann.loraine Ann Loraine added a comment -

                  Assigning to Mason to track progress on issue & notify Alex when fix is done.

                  Show
                  ann.loraine Ann Loraine added a comment - Assigning to Mason to track progress on issue & notify Alex when fix is done.

                    People

                    • Assignee:
                      mason Mason Meyer (Inactive)
                      Reporter:
                      support Support (Inactive)
                    • Votes:
                      0 Vote for this issue
                      Watchers:
                      3 Start watching this issue

                      Dates

                      • Created:
                        Updated:
                        Resolved: