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kjaisinghkjaisingh
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Modify genotype filtering to ingest cutoffs from a table (#864)
1 parent 8d48278 commit 3ce0ddd

29 files changed

+566
-428
lines changed

‎.github/.dockstore.yml‎

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@@ -171,6 +171,15 @@ workflows:
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tags:
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- /.*/
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- subclass: WDL
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name: ScoreGenotypes
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primaryDescriptorPath: /wdl/ScoreGenotypes.wdl
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filters:
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branches:
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- main
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tags:
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- /.*/
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- subclass: WDL
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name: FilterGenotypes
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primaryDescriptorPath: /wdl/FilterGenotypes.wdl

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

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@@ -2,24 +2,8 @@
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"FilterGenotypes.vcf": "${this.concordance_vcf}",
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"FilterGenotypes.output_prefix": "${this.sample_set_set_id}",
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"FilterGenotypes.ploidy_table": "${this.ploidy_table}",
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"FilterGenotypes.gq_recalibrator_model_file": "${workspace.recalibrate_gq_model_file}",
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"FilterGenotypes.sl_filter_args": "--small-del-threshold 93 --medium-del-threshold 150 --small-dup-threshold -51 --medium-dup-threshold -4 --ins-threshold -13 --inv-threshold -19",
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"FilterGenotypes.genome_tracks": [
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{{ reference_resources.recalibrate_gq_genome_track_repeatmasker | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_segdup | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_simple_repeats | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_umap100 | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_umap24 | tojson }}
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],
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"FilterGenotypes.recalibrate_gq_args": [
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"--keep-homvar false",
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"--keep-homref true",
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"--keep-multiallelic true",
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"--skip-genotype-filtering true",
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"--min-samples-to-estimate-allele-frequency -1"
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],
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"FilterGenotypes.sl_cutoff_table": "${workspace.sl_cutoff_table}",
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"FilterGenotypes.ped_file": "${workspace.cohort_ped_file}",
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"FilterGenotypes.primary_contigs_fai": "${workspace.primary_contigs_fai}",
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"FilterGenotypes.site_level_comparison_datasets": [
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"disk_gb": 100
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},
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"FilterGenotypes.linux_docker": "${workspace.linux_docker}",
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"FilterGenotypes.gatk_docker": "${workspace.gq_recalibrator_docker}",
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"FilterGenotypes.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
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"FilterGenotypes.sv_pipeline_docker": "${workspace.sv_pipeline_docker}"
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}

‎inputs/templates/terra_workspaces/cohort_mode/workflow_configurations/ScoreGenotypes.tmpl‎

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@@ -0,0 +1,25 @@
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{
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"ScoreGenotypes.vcf": "${this.concordance_vcf}",
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"ScoreGenotypes.output_prefix": "${this.sample_set_set_id}",
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"ScoreGenotypes.gq_recalibrator_model_file": "${workspace.recalibrate_gq_model_file}",
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"ScoreGenotypes.recalibrate_gq_args": [
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"--keep-homvar false",
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"--keep-homref true",
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"--keep-multiallelic true",
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"--skip-genotype-filtering true",
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"--min-samples-to-estimate-allele-frequency -1"
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],
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"ScoreGenotypes.genome_tracks": [
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{{ reference_resources.recalibrate_gq_genome_track_repeatmasker | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_segdup | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_simple_repeats | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_umap100 | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_umap24 | tojson }}
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],
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"ScoreGenotypes.linux_docker": "${workspace.linux_docker}",
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"ScoreGenotypes.gatk_docker": "${workspace.gq_recalibrator_docker}",
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"ScoreGenotypes.sv_base_mini_docker": "${workspace.sv_base_mini_docker}",
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"ScoreGenotypes.sv_pipeline_docker": "${workspace.sv_pipeline_docker}"
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}

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

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@@ -60,6 +60,7 @@ reference_version {{ reference_resources.reference_version }}
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rmsk {{ reference_resources.rmsk }}
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segdups {{ reference_resources.segdups }}
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seed_cutoffs {{ reference_resources.seed_cutoffs }}
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sl_cutoff_table {{ reference_resources.sl_cutoff_table }}
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stratification_config_part1 {{ reference_resources.stratification_config_part1 }}
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stratification_config_part2 {{ reference_resources.stratification_config_part2 }}
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wgd_scoring_mask {{ reference_resources.wgd_scoring_mask }}

‎inputs/templates/terra_workspaces/single_sample/GATKSVPipelineSingleSample.json.tmpl‎

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"GATKSVPipelineSingleSample.RefineComplexVariants.n_per_split": "15000",
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"GATKSVPipelineSingleSample.gq_recalibrator_model_file": "${workspace.recalibrate_gq_model_file}",
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"GATKSVPipelineSingleSample.sl_cutoff_table": "${workspace.sl_cutoff_table}",
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"GATKSVPipelineSingleSample.sl_filter_args": "--gq-scale-factor 1.012072 --upper-sl-cap 1500 --lower-sl-cap -1000 --sl-shift 300",
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"GATKSVPipelineSingleSample.genome_tracks": [
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{{ reference_resources.recalibrate_gq_genome_track_repeatmasker | tojson }},

‎inputs/templates/terra_workspaces/single_sample/workspace.tsv.tmpl‎

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@@ -84,5 +84,6 @@ reference_segdups {{ reference_resources.segdups }}
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reference_seed_cutoffs {{ reference_resources.seed_cutoffs }}
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reference_wgd_scoring_mask {{ reference_resources.wgd_scoring_mask }}
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reference_wham_include_list_bed_file {{ reference_resources.wham_include_list_bed_file }}
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sl_cutoff_table {{ reference_resources.sl_cutoff_table }}
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stratification_config_part1 {{ reference_resources.stratification_config_part1 }}
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stratification_config_part2 {{ reference_resources.stratification_config_part2 }}

‎inputs/templates/test/FilterGenotypes/FilterGenotypes.fixed_cutoffs.json.tmpl‎

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@@ -2,24 +2,8 @@
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"FilterGenotypes.vcf": {{ test_batch.concordance_vcf | tojson }},
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"FilterGenotypes.output_prefix": {{ test_batch.name | tojson }},
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"FilterGenotypes.ploidy_table": {{ test_batch.ploidy_table | tojson }},
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"FilterGenotypes.gq_recalibrator_model_file": {{ reference_resources.aou_recalibrate_gq_model_file | tojson }},
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"FilterGenotypes.sl_filter_args": "--small-del-threshold 93 --medium-del-threshold 150 --small-dup-threshold -51 --medium-dup-threshold -4 --ins-threshold -13 --inv-threshold -19",
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"FilterGenotypes.genome_tracks": [
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{{ reference_resources.recalibrate_gq_genome_track_repeatmasker | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_segdup | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_simple_repeats | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_umap100 | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_umap24 | tojson }}
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],
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"FilterGenotypes.recalibrate_gq_args": [
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"--keep-homvar false",
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"--keep-homref true",
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"--keep-multiallelic true",
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"--skip-genotype-filtering true",
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"--min-samples-to-estimate-allele-frequency -1"
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],
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"FilterGenotypes.sl_cutoff_table": {{ test_batch.sl_cutoff_table | tojson }},
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"FilterGenotypes.ped_file": {{ test_batch.ped_file | tojson }},
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"FilterGenotypes.primary_contigs_fai": {{ reference_resources.primary_contigs_fai | tojson }},
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"FilterGenotypes.site_level_comparison_datasets": [
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"disk_gb": 100
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},
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"FilterGenotypes.linux_docker": {{ dockers.linux_docker | tojson }},
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"FilterGenotypes.gatk_docker": {{ dockers.gq_recalibrator_docker | tojson }},
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"FilterGenotypes.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
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"FilterGenotypes.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }}
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}

‎inputs/templates/test/FilterGenotypes/FilterGenotypes.optimize_cutoffs.json.tmpl‎

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@@ -2,26 +2,10 @@
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"FilterGenotypes.vcf": {{ test_batch.concordance_vcf | tojson }},
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"FilterGenotypes.output_prefix": {{ test_batch.name | tojson }},
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"FilterGenotypes.ploidy_table": {{ test_batch.ploidy_table | tojson }},
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"FilterGenotypes.truth_json": {{ test_batch.recalibrate_gq_truth_json | tojson }},
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"FilterGenotypes.primary_contigs_fai": {{ reference_resources.primary_contigs_fai | tojson }},
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"FilterGenotypes.gq_recalibrator_model_file": {{ reference_resources.aou_recalibrate_gq_model_file | tojson }},
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"FilterGenotypes.genome_tracks": [
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{{ reference_resources.recalibrate_gq_genome_track_repeatmasker | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_segdup | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_simple_repeats | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_umap100 | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_umap24 | tojson }}
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],
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"FilterGenotypes.recalibrate_gq_args": [
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"--keep-homvar false",
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"--keep-homref true",
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"--keep-multiallelic true",
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"--skip-genotype-filtering true",
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"--min-samples-to-estimate-allele-frequency -1"
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],
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"FilterGenotypes.sl_cutoff_table": {{ test_batch.sl_cutoff_table | tojson }},
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"FilterGenotypes.ped_file": {{ test_batch.ped_file | tojson }},
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"FilterGenotypes.primary_contigs_fai": {{ reference_resources.primary_contigs_fai | tojson }},
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"FilterGenotypes.site_level_comparison_datasets": [
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{{ reference_resources.ccdg_abel_site_level_benchmarking_dataset | tojson }},
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{{ reference_resources.gnomad_v4_site_level_benchmarking_dataset | tojson }},
@@ -38,8 +22,6 @@
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"disk_gb": 50
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},
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"FilterGenotypes.linux_docker": {{ dockers.linux_docker | tojson }},
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"FilterGenotypes.gatk_docker": {{ dockers.gq_recalibrator_docker | tojson }},
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"FilterGenotypes.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
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"FilterGenotypes.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }}
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}

‎inputs/templates/test/GATKSVPipelineSingleSample/GATKSVPipelineSingleSample.json.tmpl‎

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"GATKSVPipelineSingleSample.gq_recalibrator_model_file": {{ reference_resources.hgsvc_release3_gq_model_file | tojson }},
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"GATKSVPipelineSingleSample.sl_filter_args": "--gq-scale-factor 1.012072 --upper-sl-cap 1500 --lower-sl-cap -1000 --sl-shift 300",
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"GATKSVPipelineSingleSample.sl_cutoff_table": {{ ref_panel.sl_cutoff_table | tojson }},
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"GATKSVPipelineSingleSample.genome_tracks": [
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{{ reference_resources.recalibrate_gq_genome_track_repeatmasker | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_segdup | tojson }},

‎inputs/templates/test/ScoreGenotypes/ScoreGenotypes.fixed_cutoffs.json.tmpl‎

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{
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"ScoreGenotypes.vcf": {{ test_batch.concordance_vcf | tojson }},
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"ScoreGenotypes.output_prefix": {{ test_batch.name | tojson }},
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"ScoreGenotypes.gq_recalibrator_model_file": {{ reference_resources.aou_recalibrate_gq_model_file | tojson }},
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"ScoreGenotypes.recalibrate_gq_args": [
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"--keep-homvar false",
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"--keep-homref true",
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"--keep-multiallelic true",
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"--skip-genotype-filtering true",
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"--min-samples-to-estimate-allele-frequency -1"
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],
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"ScoreGenotypes.genome_tracks": [
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{{ reference_resources.recalibrate_gq_genome_track_repeatmasker | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_segdup | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_simple_repeats | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_umap100 | tojson }},
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{{ reference_resources.recalibrate_gq_genome_track_umap24 | tojson }}
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],
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"ScoreGenotypes.linux_docker": {{ dockers.linux_docker | tojson }},
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"ScoreGenotypes.gatk_docker": {{ dockers.gq_recalibrator_docker | tojson }},
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"ScoreGenotypes.sv_base_mini_docker": {{ dockers.sv_base_mini_docker | tojson }},
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"ScoreGenotypes.sv_pipeline_docker": {{ dockers.sv_pipeline_docker | tojson }}
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}

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