gatk-sv
gatk-sv copied to clipboard
broadinstitute
A structural variation pipeline for short-read sequencing
How can I apply downstream filtering steps (minGQ filtering, FilterOutlierSamples, BatchEffect, and FilterCleanupQualRecalibration) to the cleaned VCF to further control the false discovery rate?
[This script](https://github.com/broadinstitute/gatk-sv/blob/master/src/sv-pipeline/04_variant_resolution/scripts/process_posthoc_cpx_depth_regenotyping.sh) is not scaling well in larger cohorts (>10K samples) and should be reimplemented in Python. It is called from the `ParseGenotypes` tasks in `GenotypeCpxCnvs.wdl` (subworkflow call stack `MakeCohortVcf.wdl`...
Many files types such as VCFs, CRAMS, BED, and evidence data files have companion index files that are sometimes required for fast retrieval over specific genomic intervals. ### Overview: Some...
A subset of dispersed duplication calls actually also have a large deletion at the insertion point, but not all are labelled correctly as ddup_idel.
@xuefzhao reported a handful of duplicated INV records in the "cleaned" vcf. I'd speculate that these the duplicates are being derived from BND records in ResolveComplexVariants, but this needs to...
Most events are real dispersed duplicated inverted insertions that should be marked as resolved complex insertions. We suspect the unresolved labeling is happening within GenotypeComplexVariants.
Tabix will crash if the resulting index filename is longer than 255 characters. This was observed in the `ResetFilter` task of the single sample pipeline: ``` tbx_index_build failed: sample_id.filter_by_ref_panel.reset_HIGH_SR_BACKGROUND_filter.reset_BOTHSIDES_SUPPORT_filter.reset_PESR_GT_OVERDISPERSION_filter.sample_qc.vcf.gz ```...
Hello. I am currently trying to build the docker image with targets `sv-pipeline` but I have been running into some issues. When I run `python build_docker.py --targets sv-pipeline --image-tag my-branch-a3fd92...
We encountered some troubles in the process of testing the GWAS-SVs pipeline with the GATK due to the lack of JSON files for module7. I wonder if you can share...
These have not been reviewed. @cwhelan left some comments on 07 in PR #51 that should be addressed.
Metadata
Owner
Metadata
A structural variation pipeline for short-read sequencing