From 5eadb0e914d86007967aacde0408c22b8e9cc60c Mon Sep 17 00:00:00 2001 From: Karan Jaisingh Date: Tue, 7 Jan 2025 22:34:09 -0500 Subject: [PATCH 1/2] Initial commit --- website/docs/modules/merge_batch_sites.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/website/docs/modules/merge_batch_sites.md b/website/docs/modules/merge_batch_sites.md index c1f789c09..7620d7e67 100644 --- a/website/docs/modules/merge_batch_sites.md +++ b/website/docs/modules/merge_batch_sites.md @@ -59,7 +59,7 @@ section apply here. Array of filtered depth VCFs across batches generated in [FilterBatch](./fb#filtered_depth_vcf). #### `pesr_vcfs` -Array of filtered depth VCFs across batches generated in [FilterBatch](./fb#filtered_pesr_vcf). +Array of filtered PE/SR VCFs across batches generated in [FilterBatch](./fb#filtered_pesr_vcf). ### Outputs From fe1672c682e86148469faef341e0651a3555b0db Mon Sep 17 00:00:00 2001 From: Karan Jaisingh Date: Thu, 9 Jan 2025 15:43:18 -0500 Subject: [PATCH 2/2] Remove filtering from GenerateBatchMetrics docs --- website/docs/execution/joint.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/website/docs/execution/joint.md b/website/docs/execution/joint.md index 4105e4edc..20569449d 100644 --- a/website/docs/execution/joint.md +++ b/website/docs/execution/joint.md @@ -66,7 +66,7 @@ algorithms (Manta, MELT, and Wham), read depth (RD), split read positions (SR), 6. `04-GatherBatchEvidence`: Per-batch copy number variant calling using cn.MOPS and GATK gCNV; B-allele frequency (BAF) generation; call and evidence aggregation 7. `05-ClusterBatch`: Per-batch variant clustering -8. `06-GenerateBatchMetrics`: Per-batch variant filtering, metric generation +8. `06-GenerateBatchMetrics`: Per-batch metric generation 9. `07-FilterBatchSites`: Per-batch variant filtering and plot SV counts per sample per SV type to enable choice of IQR cutoff for outlier filtration in `08-FilterBatchSamples` 10. `08-FilterBatchSamples`: Per-batch outlier sample filtration