Mark Walker

Peg GATK release in sv-base Dockerfile

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We can first use a permanent commit from master once `PrintSVEvidence` is merged (currently a commit hash is used, which may change if the branch is deleted or rebased). Ultimately...

Use GATK to retrieve VCF records in JoinContigFromRemoteVcfs

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This almost-working code can replace remote tabix, but there are a few issues: 1. Downstream scripts expect empty format fields to be present (as ".") but GATK removes them 2....

Need to address @cwhelan's comments from #216 in a separate PR.

SV clustering uses both reciprocal overlap and a maximum endpoint distance criteria. Currently, calls with only depth evidence are clustered differently from other classes in that only one of these...

Adds an option to SVCluster to disable output sorting/indexing. Since sorting requires holding an indeterminate number of records in memory, it can substantially inflate memory usage. Analagous to #8623.

Replaces most methods in the CombineBatches workflow with a greatly simplified set of tasks that utilize GATK `SVCluster` and the new `GroupedSVCluster` tool (see [PR](https://github.com/broadinstitute/gatk/pull/8990)). `SVCluster` replaces most of the...

We will move almost all content from the main README and Terra dashboards into the website to reduce redundancy and avoid discrepancies. A few specific items from #695: - Remove...

Need program permission and testing on an independent dataset.

Updates methods for Scramble calling. This includes several critical components: 1. Filtering of calls within reference MEIs overlapping indels and small deletion SVs. This was a major source of false...

Implements two new tools and updates some methods for a revamp of the `CombineBatches` cross-batch integration module in [gatk-sv](https://github.com/broadinstitute/gatk-sv). - `SVStratify` - tool for splitting out a VCF by variant...