gatk-sv
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broadinstitute
A structural variation pipeline for short-read sequencing
Relates to #661 This issue is better explained there - as far as I can see the AD processing script includes the possibility of generating float values for an Integer...
We want to add GD region overlap to the INFO field. It seems to make sense to do this in AnnotateVcf, probably within SVAnnotate. We could add a separate reference...
When svtk vcfcluster merges records, it creates lists of INFO values from the member records, even when the Number for the INFO key defined in the header is 1 ([link](https://github.com/broadinstitute/gatk-sv/blob/d37e453038e425acba9683da503218fe3d4b1033/src/svtk/svtk/svfile.py#L302))....
This is supposed to be done in CleanVcf1a but it does not appear to be working, perhaps as a result of a downstream step.
### Updates New workflow to remove outlier samples. * Uses `src/sv-pipeline/scripts/downstream_analysis_and_filtering/determine_svcount_outliers.R` for plotting and outlier determination which only considers SV types with a median SVs per sample of at least...
svtk vcf2bed uses the ALT field to produce the `svtype` column in the output BED file. This means that the `svtype` column includes BND alt alleles and values like INS:ME...
### Instructions Hi, I had successfully installed svtk and used it correctly, but I'm not sure why it stopped working properly after some time. I wonder if I updated some...
## Bug Report ### Affected module(s) or script(s) wdl/GatherSampleEvidence ### Affected version(s) This codebase as-of [this commit](https://github.com/broadinstitute/gatk-sv/pull/605) ### Description I've seen a couple of failing jobs recently where ScramblePart1 is...
Hello. I was wondering if there is any documentation on the role each parameter plays within the overall code. I am trying to use GATK-SV to identify de novo structural...
A recent large cohort had more CPX events > 1Mb than expected. The RD plots for the large CNVs within these complex SVs don't show visible changes in read depth....
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A structural variation pipeline for short-read sequencing