gatk-sv

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Workflows for reclustering CNVs in repetitive regions. This is intended as a temporary solution for cleaning up redundant calls post-filtering, but I'm providing it here for use with ongoing projects...

mwalker174

Pulls in 2 updated workflows for batch effect detection that were used for gnomAD-v3. Here I have successfully tested them on a small cross-section of the data (a few hundred...

mwalker174

This PR is about an alpha version of a report generator that I coded to generate a report using the plots generated in "*.pdf, *.jpg, and *.png" formats in a...

shadizaheri

krithikanathamuni

- Pegged GATK jar embedded in the sv-pipeline dockers to the latest release (4.2.6.1) per #81. - Removed tabix commands, which are automatically generated by PrintSVEvidence. - Removed unneeded `gatk_docker_pesr_override`...

mwalker174

END fields

1

The END info field is currently misused throughout much of the pipeline. According to the [VCF specification](https://samtools.github.io/hts-specs/VCFv4.2.pdf), the END tag is defined as: ```end position of variant described in this...

mwalker174

GenotypeBatch: svtk count error

2

[Files_for_gatksv_issue.tar.gz](https://github.com/broadinstitute/gatk-sv/files/8398892/Files_for_gatksv_issue.tar.gz) ## Bug Report ### Affected module(s) or script(s) _Module/script name(s), special parameters?_ call-GenotypeBatch -> call-GenotypePESRPart2 -> call-CountSRBca ### Affected version(s) - [ ] Latest master branch as of [Feb...

arosato87

Strange results for pe- and sr-tests

5

Hello again! 1) I've got a result from GATK CollectSVEvidence for single sample - everything is okay. 2) Then i standardized my vcf files from manta and delly in svtk-pipeline...

NstVasileva

Need clearer instructions on each parameter for GATK-SV-single-sample

2

Hi, I'm trying to use the workspace help-gatk/GATK-Structural-Variants-Single-Sample](https://anvil.terra.bio/#workspaces/help-gatk/GATK-Structural-Variants-Single-Sample to call SVs on a few individuals I have. I decided to use the 1000G reference panel on https://console.cloud.google.com/storage/browser/gatk-sv-resources-public?authuser=0 but this still...

jasonbhn

All sv are filtered out at TrainPEGenotyping step.

2

Hi, I'm trying to replicate the gatk-sv workflow with snakemake and encountered a problem at the TrainPEGenotyping step. At the step of generating the $batch.pe.train.include.txt in PE_genotype.sh script, all variants...

giacuong171