gatk-sv
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broadinstitute
A structural variation pipeline for short-read sequencing
Dear Authors, The error below is being triggered during building docker image from `gatksv/sv-base:b3af2e3` to build `MELT` docker image specifically while updating `RUN apt-get -qqy dist-upgrade && ` ``` W:...
The `--split-bnd` option causes BND records to be broken into two records: one for the start and one for the end. `svtk vcf2bed` currently uses the `END` position but should...
Quick update to a utility script that traverses a Cromwell metadata file and generates input/output jsons for all subworkflows. In particular, this update enables the script to emit the input...
Use of cloud-specific commands (i.e. `gsutil`, `gcloud`) need to be removed or abstracted to scripts in order to support different cloud platforms. There are currently 7 uses of `gsutil` within...
## Feature request ### EvidenceQC New relatedness analysis at EvidenceQC module ### Description Request to add relatedness checks at an early stage of the pipeline. A suggestion could be to...
Adds a new workflow for transferring INFO and FORMAT field annotations from one vcf to another. The implementation is efficient in that it traverses the two vcfs together to minimize...
## Feature request ### Module(s) or script(s) involved AnnotateVcf Module ### Description Could we please add gnomAD allele counts in addition to the gnomad allele frequency?
Hi! Thank you for sharing this extraordinary pipeline. Tried with some samples and the outcomes were amazingly satisfactory. As we are planning to switch to analysis based on the new...
During the course of working on https://github.com/broadinstitute/gatk-sv/issues/520 I noticed what looks like a possible logic/processing error in `src/sv-pipeline/04_variant_resolution/scripts/IntegrateGQ.sh`. The script starts by creating a bed file from the input VCF:...
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A structural variation pipeline for short-read sequencing