[VS-693] Add support for VQSR Lite to GvsCreateFilterSet (#8157)

* Added a new suite of tools for variant filtering based on site-level annotations. (#7954)

* Adds wdl that tests joint VCF filtering tools (#7932)

* adding filtering wdl

* renaming pipeline

* addressing comments

* added bash

* renaming json

* adding glob to extract for extra files

* changing dollar signs

* small comments

* Added changes for specifying model backend and other tweaks to WDLs and environment.

* Added classes for representing a collection of labeled variant annotations.

* Added interfaces for modeling and scoring backends.

* Added a new suite of tools for variant filtering based on site-level annotations.

* Added integration tests.

* Added test resources and expected results.

* Miscellaneous changes.

* Removed non-ASCII characters.

* Added documentation for TrainVariantAnnotationsModel and addressed review comments.

Co-authored-by: meganshand <[email protected]>

* Added toggle for selecting resource-matching strategies and miscellaneous minor fixes to new annotation-based filtering tools. (#8049)

* Adding use_allele_specific_annotation arg and fixing task with empty input in JointVcfFiltering WDL (#8027)

* Small changes to JointVCFFiltering WDL

* making default for use_allele_specific_annotations

* addressing comments

* first stab

* wire through WDL changes

* fixed typo

* set model_backend input value

* add gatk_override to JointVcfFiltering call

* typo in indel_annotations

* make model_backend optional

* tabs and spaces

* make all model_backends optional

* use gatk 4.3.0

* no point in changing the table names as this is a POC

* adding new branch to dockstore

* adding in branching logic for classic VQSR vs VQSR-Lite

* implementing the separate schemas for the VQSR vs VQSR-Lite branches, including Java changes necessary to produce the different tsv files

* passing classic flag to indel run of CreateFilteringFiles

* Update GvsCreateFilterSet.wdl

cleaning up verbiage

* Removed mapping error rate from estimate of denoised copy ratios output by gCNV and updated sklearn. (#7261)

* cleanup up sloppy comment

---------

Co-authored-by: samuelklee <[email protected]>
Co-authored-by: meganshand <[email protected]>
Co-authored-by: Rebecca Asch <[email protected]>

.dockstore.yml

@@ -95,6 +95,8 @@ workflows:
        branches:
          - master
          - ah_var_store
+         - rsa_vqsr_lite_poc
+         - VS-693_VQSR_lite
    - name: GvsPopulateAltAllele
      subclass: WDL
      primaryDescriptorPath: /scripts/variantstore/wdl/GvsPopulateAltAllele.wdl

.github/workflows/gatk-tests.yml

@@ -291,7 +291,7 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        wdlTest: [ 'RUN_CNV_GERMLINE_COHORT_WDL', 'RUN_CNV_GERMLINE_CASE_WDL', 'RUN_CNV_SOMATIC_WDL', 'RUN_M2_WDL', 'RUN_CNN_WDL' ]
+        wdlTest: [ 'RUN_CNV_GERMLINE_COHORT_WDL', 'RUN_CNV_GERMLINE_CASE_WDL', 'RUN_CNV_SOMATIC_WDL', 'RUN_M2_WDL', 'RUN_CNN_WDL', 'RUN_VCF_SITE_LEVEL_FILTERING_WDL' ]
     continue-on-error: true
     name: WDL test ${{ matrix.wdlTest }} on cromwell
     steps:
@@ -349,3 +349,9 @@ jobs:
         run: |
           echo "Running CNN WDL";
           bash scripts/cnn_variant_cromwell_tests/run_cnn_variant_wdl.sh;
+
+      - name: "VCF_SITE_LEVEL_FILTERING_WDL_TEST"
+        if: ${{ matrix.wdlTest == 'RUN_VCF_SITE_LEVEL_FILTERING_WDL' }}
+        run: |
+          echo "Running VCF Site Level Filtering WDL";
+          bash scripts/vcf_site_level_filtering_cromwell_tests/run_vcf_site_level_filtering_wdl.sh;

build.gradle

@@ -293,6 +293,7 @@ dependencies {
 
     implementation 'org.apache.commons:commons-lang3:3.5'
     implementation 'org.apache.commons:commons-math3:3.5'
+    implementation 'org.hipparchus:hipparchus-stat:2.0'
     implementation 'org.apache.commons:commons-collections4:4.1'
     implementation 'org.apache.commons:commons-vfs2:2.0'
     implementation 'org.apache.commons:commons-configuration2:2.4'

scripts/gatkcondaenv.yml.template

@@ -38,10 +38,11 @@ dependencies:
                                     #   if you wish to update, note that versions of conda-forge::keras after 2.2.5
                                     #   undesirably set the environment variable KERAS_BACKEND = theano by default
 - defaults::intel-openmp=2019.4
-- conda-forge::scikit-learn=0.22.2
+- conda-forge::scikit-learn=0.23.1
 - conda-forge::matplotlib=3.2.1
 - conda-forge::pandas=1.0.3
 - conda-forge::typing_extensions=4.1.1   # see https://github.com/broadinstitute/gatk/issues/7800 and linked PRs
+- conda-forge::dill=0.3.4                # used for pickling lambdas in TrainVariantAnnotationsModel
 
 # core R dependencies; these should only be used for plotting and do not take precedence over core python dependencies!
 - r-base=3.6.2

scripts/vcf_site_level_filtering_cromwell_tests/README.md

@@ -0,0 +1,9 @@
+# Filtering Automated Tests for WDL
+
+**This directory is for GATK devs only**
+
+This directory contains scripts for running Variant Site Level WDL tests in the automated travis build environment.
+
+Please note that this only tests whether the WDL will complete successfully.
+
+Test data is a "plumbing test" using a small portion of a 10 sample callset.

scripts/vcf_site_level_filtering_cromwell_tests/run_vcf_site_level_filtering_wdl.sh

@@ -0,0 +1,38 @@
+#!/bin/bash -l
+set -e
+#cd in the directory of the script in order to use relative paths
+script_path=$( cd "$(dirname "${BASH_SOURCE}")" ; pwd -P )
+cd "$script_path"
+
+WORKING_DIR=/home/runner/work/gatk
+
+set -e
+echo "Building docker image for VCF Site Level Filtering WDL tests (skipping unit tests)..."
+
+#assume Dockerfile is in root
+echo "Building docker without running unit tests... ========="
+cd $WORKING_DIR/gatk
+
+# IMPORTANT: This code is duplicated in the cnv and M2 WDL test.
+if [ ! -z "$CI_PULL_REQUEST" ]; then
+  HASH_TO_USE=FETCH_HEAD
+  sudo bash build_docker.sh  -e ${HASH_TO_USE} -s -u -d $PWD/temp_staging/ -t ${CI_PULL_REQUEST};
+  echo "using fetch head:"$HASH_TO_USE
+else
+  HASH_TO_USE=${CI_COMMIT}
+  sudo bash build_docker.sh  -e ${HASH_TO_USE} -s -u -d $PWD/temp_staging/;
+  echo "using travis commit:"$HASH_TO_USE
+fi
+echo "Docker build done =========="
+
+cd $WORKING_DIR/gatk/scripts/
+sed -r "s/__GATK_DOCKER__/broadinstitute\/gatk\:$HASH_TO_USE/g" vcf_site_level_filtering_cromwell_tests/vcf_site_level_filtering_travis.json >$WORKING_DIR/vcf_site_level_filtering_travis.json
+echo "JSON FILES (modified) ======="
+cat $WORKING_DIR/vcf_site_level_filtering_travis.json
+echo "=================="
+
+
+echo "Running Filtering WDL through cromwell"
+ln -fs $WORKING_DIR/gatk/scripts/vcf_site_level_filtering_wdl/JointVcfFiltering.wdl
+cd $WORKING_DIR/gatk/scripts/vcf_site_level_filtering_wdl/
+java -jar $CROMWELL_JAR run JointVcfFiltering.wdl -i $WORKING_DIR/vcf_site_level_filtering_travis.json

scripts/vcf_site_level_filtering_cromwell_tests/vcf_site_level_filtering_travis.json

@@ -0,0 +1,14 @@
+{
+  "JointVcfFiltering.gatk_docker": "__GATK_DOCKER__",
+  "JointVcfFiltering.vcf": ["/home/runner/work/gatk/gatk/src/test/resources/large/filteringJointVcf/test_10_samples.22.avg.vcf.gz",
+    "/home/runner/work/gatk/gatk/src/test/resources/large/filteringJointVcf/test_10_samples.23.avg.vcf.gz"],
+  "JointVcfFiltering.vcf_index": ["/home/runner/work/gatk/gatk/src/test/resources/large/filteringJointVcf/test_10_samples.22.avg.vcf.gz.tbi",
+    "/home/runner/work/gatk/gatk/src/test/resources/large/filteringJointVcf/test_10_samples.23.avg.vcf.gz.tbi"],
+  "JointVcfFiltering.sites_only_vcf": "/home/runner/work/gatk/gatk/src/test/resources/large/filteringJointVcf/test_10_samples.sites_only.vcf.gz",
+  "JointVcfFiltering.sites_only_vcf_index": "/home/runner/work/gatk/gatk/src/test/resources/large/filteringJointVcf/test_10_samples.sites_only.vcf.gz.tbi",
+  "JointVcfFiltering.basename": "test_10_samples",
+  "JointVcfFiltering.snp_annotations": "-A ReadPosRankSum -A FS -A SOR -A QD -A AVERAGE_TREE_SCORE -A AVERAGE_ASSEMBLED_HAPS -A AVERAGE_FILTERED_HAPS",
+  "JointVcfFiltering.indel_annotations": "-A MQRankSum -A ReadPosRankSum -A FS -A SOR -A QD -A AVERAGE_TREE_SCORE",
+  "JointVcfFiltering.model_backend": "PYTHON_IFOREST",
+  "JointVcfFiltering.use_allele_specific_annotations": false
+}