Mark Walker
Mark Walker
Analogous to GenotypeConcordance, but for SVs.
## Feature request ### Tool(s) or class(es) involved Docker image ### Description We've been using this function in the GATK-SV WDLs to estimate the appropriate `-XmX` Java parameter for GATK...
OS Ubuntu 18.04 (within a docker container) htslib v1.10.2 compiled from source (also when installed from the v0.7 apt package) gcloud SDK v235.0.0-0 installed from apt package We have a...
- Complex (CPX) SV records no longer use `END2`/`CHR2` INFO fields and instead are defined by `CPX_INTERVALS` in addition to normal coordinates. - Adds new class `SVCallRecord.ComplexEventInterval` for storing complex...
We are observing non-deterministic behavior of `whamg` when run multiple times across cloud VMs on the same BAM file, where about 5-10% of calls are different. I see from a...
This is supposed to be done in CleanVcf1a but it does not appear to be working, perhaps as a result of a downstream step.
Adds a call to `ReshardVcf` at the end of `ResolveComplexVariants`. In addition, each of the `BOTHSIDES_PASS` and `HIGH_SR_BACKGROUND` contig-sharded variant tables is concatenated into a single genome-wide table prior to...
A critical optimization to the `ParseGenotypes` task that reimplements `process_posthoc_cpx_depth_regenotyping.py` with greatly accelerated computations. The previous version of the script used many repetitive quadratic (N^2) commands that caused it to...
[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...