Filter wham-only DELs and scramble-only SVAs in CleanVcf & docs updates (#740)

Author: epiercehoffman

.github/.dockstore.yml

@@ -198,6 +198,15 @@ workflows:
       tags:
         - /.*/
 
+  - subclass: WDL
+    name: VisualizeCnvs
+    primaryDescriptorPath: /wdl/VisualizeCnvs.wdl
+    filters:
+      branches:
+        - main
+      tags:
+        - /.*/
+
   - subclass: WDL
     name: SingleSamplePipeline
     primaryDescriptorPath: /wdl/GATKSVPipelineSingleSample.wdl

README.md

@@ -2,7 +2,7 @@
 
 A structural variation discovery pipeline for Illumina short-read whole-genome sequencing (WGS) data.
 
-For technical documentation on GATK-SV, including how to run the pipeline, please refer to our website.
+For technical documentation on GATK-SV, including how to run the pipeline, please refer to our [website](https://broadinstitute.github.io/gatk-sv/).
 
 ## Repository structure
 * `/carrot`: [Carrot](https://github.com/broadinstitute/carrot) tests

inputs/templates/terra_workspaces/cohort_mode/cohort_mode_workspace_dashboard.md.tmpl

@@ -0,0 +1,10 @@
+{
+  "VisualizeCnvs.vcf_or_bed": "${this.filtered_vcf}",
+  "VisualizeCnvs.prefix": "${this.sample_set_set_id}",
+  "VisualizeCnvs.median_files": "${this.sample_sets.median_cov}",
+  "VisualizeCnvs.rd_files": "${this.sample_sets.merged_bincov}",
+  "VisualizeCnvs.ped_file": "${workspace.cohort_ped_file}",
+  "VisualizeCnvs.min_size": 50000,
+  "VisualizeCnvs.flags": "-s 999999999",
+  "VisualizeCnvs.sv_pipeline_docker": "${workspace.sv_pipeline_docker}"
+}

inputs/templates/terra_workspaces/cohort_mode/samples_1kgp_156.tsv.tmpl

@@ -5,6 +5,6 @@
   "VisualizeCnvs.rd_files": [{{ test_batch.merged_coverage_file | tojson }}],
   "VisualizeCnvs.ped_file": {{ test_batch.ped_file | tojson }},
   "VisualizeCnvs.min_size": 50000,
-  "VisualizeCnvs.flags": "",
+  "VisualizeCnvs.flags": "-s 999999999",
   "VisualizeCnvs.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }}
 }

…spaces/cohort_mode/samples_1kgp.tsv.tmpl …es/cohort_mode/samples_1kgp_312.tsv.tmplinputs/templates/terra_workspaces/cohort_mode/samples_1kgp.tsv.tmpl renamed to inputs/templates/terra_workspaces/cohort_mode/samples_1kgp_312.tsv.tmpl inputs/templates/terra_workspaces/cohort_mode/samples_1kgp.tsv.tmpl renamed to inputs/templates/terra_workspaces/cohort_mode/samples_1kgp_312.tsv.tmpl

@@ -113,7 +113,7 @@ def main():
     parser.add_argument("-j", "--womtool-jar", help="Path to womtool jar", required=True)
     parser.add_argument("-n", "--num-input-jsons",
                         help="Number of Terra input JSONs expected",
-                        required=False, default=25, type=int)
+                        required=False, default=26, type=int)
     parser.add_argument("--log-level",
                         help="Specify level of logging information, ie. info, warning, error (not case-sensitive)",
                         required=False, default="INFO")

inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/VisualizeCnvs.json.tmpl

@@ -53,6 +53,7 @@ workflow CleanVcfChromosome {
     RuntimeAttr? runtime_override_stitch_fragmented_cnvs
     RuntimeAttr? runtime_override_final_cleanup
     RuntimeAttr? runtime_override_rescue_me_dels
+    RuntimeAttr? runtime_attr_add_high_fp_rate_filters
 
     # Clean vcf 1b
     RuntimeAttr? runtime_attr_override_subset_large_cnvs_1b
@@ -299,9 +300,17 @@ workflow CleanVcfChromosome {
       runtime_attr_override = runtime_override_rescue_me_dels
   }
 
-  call FinalCleanup {
+  call AddHighFDRFilters {
     input:
       vcf=RescueMobileElementDeletions.out,
+      prefix="~{prefix}.high_fdr_filtered",
+      sv_pipeline_docker=sv_pipeline_docker,
+      runtime_attr_override=runtime_attr_add_high_fp_rate_filters
+  }
+
+  call FinalCleanup {
+    input:
+      vcf=AddHighFDRFilters.out,
       contig=contig,
       prefix="~{prefix}.final_cleanup",
       sv_pipeline_docker=sv_pipeline_docker,
@@ -799,6 +808,58 @@ task StitchFragmentedCnvs {
   }
 }
 
+# Add FILTER status for pockets of variants with high FP rate: wham-only DELs and Scramble-only SVAs with HIGH_SR_BACKGROUND
+task AddHighFDRFilters {
+  input {
+    File vcf
+    String prefix
+    String sv_pipeline_docker
+    RuntimeAttr? runtime_attr_override
+  }
+
+  Float input_size = size(vcf, "GiB")
+  RuntimeAttr runtime_default = object {
+    mem_gb: 3.75,
+    disk_gb: ceil(10.0 + input_size * 3.0),
+    cpu_cores: 1,
+    preemptible_tries: 3,
+    max_retries: 1,
+    boot_disk_gb: 10
+  }
+  RuntimeAttr runtime_override = select_first([runtime_attr_override, runtime_default])
+  runtime {
+    memory: "~{select_first([runtime_override.mem_gb, runtime_default.mem_gb])} GB"
+    disks: "local-disk ~{select_first([runtime_override.disk_gb, runtime_default.disk_gb])} HDD"
+    cpu: select_first([runtime_override.cpu_cores, runtime_default.cpu_cores])
+    preemptible: select_first([runtime_override.preemptible_tries, runtime_default.preemptible_tries])
+    maxRetries: select_first([runtime_override.max_retries, runtime_default.max_retries])
+    docker: sv_pipeline_docker
+    bootDiskSizeGb: select_first([runtime_override.boot_disk_gb, runtime_default.boot_disk_gb])
+  }
+
+  command <<<
+    set -euo pipefail
+
+    python <<CODE
+import pysam
+with pysam.VariantFile("~{vcf}", 'r') as fin:
+  header = fin.header
+  header.add_line("##FILTER=<ID=HIGH_ALGORITHM_FDR,Description=\"Categories of variants with low precision including Wham-only deletions and certain Scramble SVAs\">")
+  with pysam.VariantFile("~{prefix}.vcf.gz", 'w', header=header) as fo:
+    for record in fin:
+        if (record.info['ALGORITHMS'] == ('wham',) and record.info['SVTYPE'] == 'DEL') or \
+          (record.info['ALGORITHMS'] == ('scramble',) and record.info['HIGH_SR_BACKGROUND'] and record.alts == ('<INS:ME:SVA>',)):
+            record.filter.add('HIGH_ALGORITHM_FDR')
+        fo.write(record)
+CODE
+  >>>
+
+  output {
+    File out = "~{prefix}.vcf.gz"
+  }
+}
+
+
 
 # Final VCF cleanup
 task FinalCleanup {

inputs/templates/test/VisualizeCnvs/VisualizeCnvs.json.tmpl

@@ -7,6 +7,7 @@
 # Generated files
 .docusaurus
 .cache-loader
+package-lock.json
 
 # Misc
 .DS_Store