From b49c7eede19c30a6e44fa09a0ce6c502f339cd84 Mon Sep 17 00:00:00 2001 From: Mark Walker Date: Fri, 25 Oct 2024 12:56:45 -0400 Subject: [PATCH] Resolve additional comments --- website/docs/execution/joint.md | 6 +++--- website/docs/modules/genotype_batch.md | 4 ++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/website/docs/execution/joint.md b/website/docs/execution/joint.md index ee834a7b6..2d3a3e5c7 100644 --- a/website/docs/execution/joint.md +++ b/website/docs/execution/joint.md @@ -86,9 +86,9 @@ AF annotation with external population callsets Extra workflows (Not part of canonical pipeline, but included for your convenience. May require manual configuration): * `MainVcfQc`: Generate detailed call set QC plots -* `PlotSVCountsPerSample`: Plot SV counts per sample per SV type -* `FilterOutlierSamples`: Filter outlier samples (in terms of SV counts) from a single VCF. Recommended to run -* `PlotSVCountsPerSample` beforehand (configured with the single VCF you want to filter) to enable IQR cutoff choice. +* `PlotSVCountsPerSample`: Plot SV counts per sample per SV type. Recommended to run before `FilterOutlierSamples` + (configured with the single VCF you want to filter) to enable IQR cutoff choice. +* `FilterOutlierSamples`: Filter outlier samples (in terms of SV counts) from a single VCF. * `VisualizeCnvs`: Plot multi-sample depth profiles for CNVs For detailed instructions on running the pipeline in Terra, see [workflow instructions](#instructions) below. diff --git a/website/docs/modules/genotype_batch.md b/website/docs/modules/genotype_batch.md index 78af3406a..0c64733c8 100644 --- a/website/docs/modules/genotype_batch.md +++ b/website/docs/modules/genotype_batch.md @@ -7,8 +7,8 @@ slug: gb [WDL source code](https://github.com/broadinstitute/gatk-sv/blob/main/wdl/GenotypeBatch.wdl) -Genotypes a batch of samples across all variants in the cohort. Note that while the preceding step, -[MergeBatchSites](./msites), is a "cohort-level", genotyping is performed on one batch of samples at a time. +Genotypes a batch of samples across all variants in the cohort. Note that while the preceding step +[MergeBatchSites](./msites) is a "cohort-level" module, genotyping is performed on one batch of samples at a time. In brief, genotyping is performed by first training variant metric cutoffs on sites with clear evidence signatures, and then genotypes and genotype qualities are assigned based on parametric models tuned with these cutoffs. This is