Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Tidy up FreeBayes #67

Closed
fnothaft opened this issue Aug 31, 2017 · 4 comments
Closed

Tidy up FreeBayes #67

fnothaft opened this issue Aug 31, 2017 · 4 comments
Assignees
Labels
Milestone

Comments

@fnothaft
Copy link
Member

@fnothaft fnothaft commented Aug 31, 2017

  • bump to quay.io/ucsc_cgl/freebayes:1.1.0--f7597a50b4449d4a963ace565a6ca7040ae10118
  • mount reference file into docker container
  • support copying files to executor
  • run in -i mode
  • specify -region when invoking FreeBayes not necessary
  • VCF comes out mis-ordered
  • use Avocado read/contig filtering mechanism (bigdatagenomics/avocado#254)
@heuermh
Copy link
Member

@heuermh heuermh commented Sep 7, 2017

Can we include test resources from https://github.com/ekg/freebayes/tree/master/test/tiny here in cli/src/test/resources? MIT License but the test data don't have a copyright notice to include.

@heuermh heuermh modified the milestones: 0.1.0, 0.2.0 Jan 24, 2018
@heuermh
Copy link
Member

@heuermh heuermh commented Feb 14, 2018

With the fix for bigdatagenomics/avocado#254 (commit bigdatagenomics/avocado@5f720cf), do you intend that Cannoli would depend on Avocado?

@heuermh
Copy link
Member

@heuermh heuermh commented Feb 27, 2018

Taking a closer look at the freebayes command line arguments, we should always use

   --strict-vcf
                   Generate strict VCF format (FORMAT/GQ will be an int)

and should provide arguments in the Freebayes wrapper for

   -A --cnv-map FILE
                   Read a copy number map from the BED file FILE, which has
                   the format:
                      reference sequence, start, end, sample name, copy number
                   ... for each region in each sample which does not have the
                   default copy number as set by --ploidy.

   --gvcf
                   Write gVCF output, which indicates coverage in uncalled regions.

   --gvcf-chunk NUM
                   When writing gVCF output emit a record for every NUM bases.

As to the rest, I'm not sure if we should wrap all of them, or provide a bulk argument/config mechanism, or simply say if you need to provide non-default parameters, call pipe manually.

@heuermh
Copy link
Member

@heuermh heuermh commented Mar 22, 2018

Fixed by #107.

@heuermh heuermh closed this Mar 22, 2018
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
None yet
Linked pull requests

Successfully merging a pull request may close this issue.

None yet
2 participants