gatk-sv
gatk-sv copied to clipboard
broadinstitute
A structural variation pipeline for short-read sequencing
we should keep the unresolved SVs from manta tloc resolve, and cluster them in the same way as manta/wham SVs
This PR extends the docs in the following areas: - [ ] Document input and output of the de-novo pipeline; - [ ] Document the method used for de-novo variant...
## Feature request Slightly relevant to #513 ### Module(s) or script(s) involved scripts/docker/build_docker.py inputs/values/dockers.json ### Description Apologies if this is a somewhat messy issue, I'll aim to revisit and polish....
updated the AF annotation scripts to : 1. revise "pop_AF" to "AF_pop" 2. added "CN_STATUS"
### Updates Create a standalone WDL for NCR and reference artifact filters. Also removes sites with zero carriers. This script pulls code from the existing NCR calculation in apply_sl_filter.py but...
The `GatherSampleEvidence` workflow is set to run `GatherSampleEvidenceMetrics` by default. However, running that task requires setting values for the optional inputs `primary_contigs_fai` and `sv_pipeline_base_docker`. Therefore, the `GatherSampleEvidence` workflow currently fails...
This PR adds utility scripts to create test data for the pipeline, which are created either by downsampling a larger file to contain information overlapping given test regions or by...
Workflows may have different input variable names for the same inputs, or the output variable name of one workflow may not match the input variable name of its downstream workflow...
Shall we consider adding mobile element insertions as independent variant type in MainVcfQc?
The CPX_TYPE for CTX records should be CTX_PP/QQ or CTX_PQ/QP. This is expected by downstream tools like ManualReview.wdl and SVAnnotate. In a recent callset, it was observed that the CPX_TYPE...
Metadata
Owner
Metadata
A structural variation pipeline for short-read sequencing