gatk-sv

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suggestions: 1. add STRANDS information to the manta_tloc file? we can either add a patch to add it after svtk resolve , or can update svtk to add the information...

xuefzhao

Changes are needed to be able to repopulate the JoinRawCalls and SVConcordance JSONs with create_test_batch.py, including outputting new files such as the ploidy table from the Batch pipeline.

mwalker174

These are for the back end of the pipeline.

mwalker174

Dockstore has a new workflow for GitHub workflow integration using a GitHub App which they recommend migrating to: https://docs.dockstore.org/en/stable/getting-started/github-apps/migrating-workflows-to-github-apps.html The main advantage of switching over to this that I can...

cwhelan

Unresolved reviewer comments for PR 373

1

In the interest of time, some reviewer comments were left unaddressed in [PR 373](https://github.com/broadinstitute/gatk-sv/pull/373) I attempted to address all the comments that were straightforward and would not affect the basic...

TedBrookings

tracking variants that are filtered from raw output

1

## Feature request Is it possible to track variants that are in the raw calls but that don't make it into the final output? It would also be nice to...

ekarlins

https://github.com/broadinstitute/gatk-sv/blob/ef29ea1374687bd62cfd18bd9e2905944256a4c8/carrot/carrot_helper.py#L699 The latest version of carrot provides the option for [test and eval wdl dependencies](https://github.com/broadinstitute/carrot/pull/182). **If running carrot_helper with the latest version of carrot** the script will fail with "`TypeError:...

bshifaw

We have found certainly outlier samples with significantly more variants can influence variant metrics (module 2) and subsequent filtering (module 3). The challenge here is that given some family based...

hab45

In the `MakeCohortVcf` module, we added an option to use Hail to concatenate VCFs on a Spark cluster, which was greatly faster (wall time wise) than single-threaded methods. However, Spark...

mwalker174

I built build/NA12878/test/GATKSVPipelineSingleSample.no_melt.json with scripts/inputs/build_default_inputs.sh. Next, I used the following cram file ftp://ftp.sra.ebi.ac.uk/vol1/run/ERR323/ERR3239334/NA12878.final.cram and downloaded all gs:// files of GATKSVPipelineSingleSample.no_melt.json to my local server and modified the json file. GATKSVPipelineSingleSample.wdl...

c2997108