gatk-sv
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broadinstitute
A structural variation pipeline for short-read sequencing
It's going above and beyond but it strikes me that we repeat a bunch of these header strings around the codebase a bunch and it would be pretty handy to...
## Minor refactoring A regression introduced in bcftools version 1.14 caused the SingleSampleFiltering.wdl task FilterVcfBySampleGenotypeAndAddEvidenceAnnotation to fail. I made a work-around using awk, but once that regression is addressed, the...
## Minor refactor Once the PR to decrease the number of docker images is accepted, there will be redundant references to the sv_pipeline docker in terms of the old dockers...
To-be-addressed from https://github.com/talkowski-lab/gatk-sv-v1/pull/252: > * Some workflows currently require index files as inputs (e.g. module00c/CNMOPS). They should either be given default values or removed as inputs altogether. > * Some...
## Bug Report ### Affected module(s) or script(s) _Module07XfBatchEffect/**find_batch_effects.shard_helper.R**_ ### How to solve: upgrade R on docker images to R 4.1.x, the errors will disappear ### Description Background: Re-run Module07...
More feedback from clinical users: The pipeline currently annotates variants with the overall AF in gnomAD and the AF in each continental subgroup. It would be helpful to provide an...
Input templates and data from 1000G need to be added for testing multi-batch runs and generating the Terra workspace.
Module : GatherBatchEvidence Job : BAFFromGVCFs_ImportGVCFs Issue: The job is taking almost 40 hours to complete for 156 (1000 genome) samples. The script and logs for the process are attached....
## Bug Report ### Affected module(s) or script(s) GatherBatchEvidenceMetrics_PEMetrics ### Affected version(s) - [x] Latest public release version [version?] - [ ] Latest master branch as of [date of test?]...
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A structural variation pipeline for short-read sequencing