VS-776. Update to latest version of VQSR Lite. #8269
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| version 1.0 | ||
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| import "GvsWarpTasks.wdl" as Tasks | ||
| import "GvsUtils.wdl" as Utils | ||
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| workflow JointVcfFiltering { | ||
| input { | ||
| String base_name | ||
| Int num_samples_loaded | ||
| File sites_only_variant_filtered_vcf | ||
| File sites_only_variant_filtered_vcf_idx | ||
| Array[File] sites_only_variant_filtered_vcfs | ||
| Array[File] sites_only_variant_filtered_vcf_idxs | ||
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| Array[String] indel_recalibration_annotations = ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"] | ||
| Array[String] snp_recalibration_annotations = ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"] | ||
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| File interval_list = "gs://gcp-public-data--broad-references/hg38/v0/wgs_calling_regions.hg38.noCentromeres.noTelomeres.interval_list" | ||
| File? gatk_override | ||
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| Int? INDEL_VQSR_max_gaussians_override = 4 | ||
| Int? INDEL_VQSR_maximum_training_variants | ||
| Int? INDEL_VQSR_mem_gb_override | ||
| Int? SNP_VQSR_max_gaussians_override = 6 | ||
| Int? SNP_VQSR_mem_gb_override | ||
| Int? SNP_VQSR_sample_every_nth_variant | ||
| Int? SNP_VQSR_maximum_training_variants | ||
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| # This is the minimum number of samples where the SNP model will be created and applied in separate tasks | ||
| # (SNPsVariantRecalibratorClassic vs. SNPsVariantRecalibratorCreateModel and SNPsVariantRecalibratorScattered) | ||
| # For VQSR classic this is done with 20k but the 10K Stroke Anderson dataset would not work unscattered (at least | ||
| # with the default VM memory settings) so this was adjusted down to 5K. | ||
| Int snps_variant_recalibration_threshold = 5000 | ||
| } | ||
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| Array[String] snp_recalibration_tranche_values = ["100.0", "99.95", "99.9", "99.8", "99.6", "99.5", "99.4", "99.3", "99.0", "98.0", "97.0", "90.0" ] | ||
| Array[String] indel_recalibration_tranche_values = ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"] | ||
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| # reference files | ||
| # Axiom - Used only for indels | ||
| # Classic: known=false,training=true,truth=false | ||
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There was a problem hiding this comment. what does this comment (and the ones like it, below) mean?
There was a problem hiding this comment. That was from when I was trying to make sure that I had the right settings for both classic and lite. I don't think it's informative here (it was more of a one time idiot check I did), so will get rid of them. |
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| File axiomPoly_resource_vcf = "gs://gcp-public-data--broad-references/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz" | ||
| File axiomPoly_resource_vcf_index = "gs://gcp-public-data--broad-references/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi" | ||
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| # DbSNP - BOTH SNPs and INDELs. But used only as known in classic (which isn't used in Lite and so dropped in lite) | ||
| # Classic: known=true,training=false,truth=false | ||
| File dbsnp_vcf = "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf" | ||
| File dbsnp_vcf_index = "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx" | ||
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| # HapMap - SNPs | ||
| # Classic: known=false,training=true,truth=true | ||
| File hapmap_resource_vcf = "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz" | ||
| File hapmap_resource_vcf_index = "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz.tbi" | ||
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| # Mills - Indels | ||
| # Classic: known=false,training=true,truth=true | ||
| File mills_resource_vcf = "gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz" | ||
| File mills_resource_vcf_index = "gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi" | ||
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| # Omni - SNPs | ||
| # Classic: known=false,training=true,truth=true | ||
| File omni_resource_vcf = "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz" | ||
| File omni_resource_vcf_index = "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz.tbi" | ||
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| # 1000G - SNPs | ||
| # Classic: known=false,training=true,truth=false | ||
| File one_thousand_genomes_resource_vcf = "gs://gcp-public-data--broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz" | ||
| File one_thousand_genomes_resource_vcf_index = "gs://gcp-public-data--broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi" | ||
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| call Tasks.IndelsVariantRecalibrator { | ||
| input: | ||
| sites_only_variant_filtered_vcf = sites_only_variant_filtered_vcf, | ||
| sites_only_variant_filtered_vcf_index = sites_only_variant_filtered_vcf_idx, | ||
| recalibration_filename = base_name + ".indels.recal", | ||
| tranches_filename = base_name + ".indels.tranches", | ||
| recalibration_tranche_values = indel_recalibration_tranche_values, | ||
| recalibration_annotation_values = indel_recalibration_annotations, | ||
| mills_resource_vcf = mills_resource_vcf, | ||
| mills_resource_vcf_index = mills_resource_vcf_index, | ||
| axiomPoly_resource_vcf = axiomPoly_resource_vcf, | ||
| axiomPoly_resource_vcf_index = axiomPoly_resource_vcf_index, | ||
| dbsnp_resource_vcf = dbsnp_vcf, | ||
| dbsnp_resource_vcf_index = dbsnp_vcf_index, | ||
| use_allele_specific_annotations = true, | ||
| disk_size = "1000", | ||
| machine_mem_gb = INDEL_VQSR_mem_gb_override, | ||
| max_gaussians = INDEL_VQSR_max_gaussians_override, | ||
| maximum_training_variants = INDEL_VQSR_maximum_training_variants, | ||
| } | ||
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| if (num_samples_loaded > snps_variant_recalibration_threshold) { | ||
| call Tasks.SNPsVariantRecalibratorCreateModel { | ||
| input: | ||
| sites_only_variant_filtered_vcf = sites_only_variant_filtered_vcf, | ||
| sites_only_variant_filtered_vcf_index = sites_only_variant_filtered_vcf_idx, | ||
| recalibration_filename = base_name + ".snps.recal", | ||
| tranches_filename = base_name + ".snps.tranches", | ||
| model_report_filename = base_name + ".snps.model.report", | ||
| recalibration_tranche_values = snp_recalibration_tranche_values, | ||
| recalibration_annotation_values = snp_recalibration_annotations, | ||
| hapmap_resource_vcf = hapmap_resource_vcf, | ||
| hapmap_resource_vcf_index = hapmap_resource_vcf_index, | ||
| omni_resource_vcf = omni_resource_vcf, | ||
| omni_resource_vcf_index = omni_resource_vcf_index, | ||
| one_thousand_genomes_resource_vcf = one_thousand_genomes_resource_vcf, | ||
| one_thousand_genomes_resource_vcf_index = one_thousand_genomes_resource_vcf_index, | ||
| dbsnp_resource_vcf = dbsnp_vcf, | ||
| dbsnp_resource_vcf_index = dbsnp_vcf_index, | ||
| use_allele_specific_annotations = true, | ||
| disk_size = "1000", | ||
| machine_mem_gb = SNP_VQSR_mem_gb_override, | ||
| max_gaussians = SNP_VQSR_max_gaussians_override, | ||
| sample_every_nth_variant = SNP_VQSR_sample_every_nth_variant, | ||
| maximum_training_variants = SNP_VQSR_maximum_training_variants | ||
| } | ||
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| scatter (idx in range(length(sites_only_variant_filtered_vcfs))) { | ||
| call Tasks.SNPsVariantRecalibrator as SNPsVariantRecalibratorScattered { | ||
| input: | ||
| sites_only_variant_filtered_vcf = sites_only_variant_filtered_vcfs[idx], | ||
| sites_only_variant_filtered_vcf_index = sites_only_variant_filtered_vcf_idxs[idx], | ||
| recalibration_filename = base_name + ".snps." + idx + ".recal", | ||
| tranches_filename = base_name + ".snps." + idx + ".tranches", | ||
| model_report = SNPsVariantRecalibratorCreateModel.model_report, | ||
| recalibration_tranche_values = snp_recalibration_tranche_values, | ||
| recalibration_annotation_values = snp_recalibration_annotations, | ||
| hapmap_resource_vcf = hapmap_resource_vcf, | ||
| hapmap_resource_vcf_index = hapmap_resource_vcf_index, | ||
| omni_resource_vcf = omni_resource_vcf, | ||
| omni_resource_vcf_index = omni_resource_vcf_index, | ||
| one_thousand_genomes_resource_vcf = one_thousand_genomes_resource_vcf, | ||
| one_thousand_genomes_resource_vcf_index = one_thousand_genomes_resource_vcf_index, | ||
| dbsnp_resource_vcf = dbsnp_vcf, | ||
| dbsnp_resource_vcf_index = dbsnp_vcf_index, | ||
| use_allele_specific_annotations = true, | ||
| disk_size = "1000", | ||
| machine_mem_gb = SNP_VQSR_mem_gb_override | ||
| } | ||
| } | ||
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| call Tasks.GatherTranches as SNPGatherTranches { | ||
| input: | ||
| tranches = SNPsVariantRecalibratorScattered.tranches, | ||
| output_filename = base_name + ".snps.gathered.tranches", | ||
| output_tranche_values = snp_recalibration_tranche_values, | ||
| mode = "SNP", | ||
| disk_size = "200", | ||
| gatk_override = gatk_override | ||
| } | ||
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| call Utils.MergeVCFs as MergeRecalibrationFiles { | ||
| input: | ||
| input_vcfs = SNPsVariantRecalibratorScattered.recalibration, | ||
| gather_type = "CONVENTIONAL", | ||
| output_vcf_name = "${base_name}.vrecalibration.vcf.gz", | ||
| preemptible_tries = 3, | ||
| } | ||
| } | ||
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| if (num_samples_loaded <= snps_variant_recalibration_threshold) { | ||
| call Tasks.SNPsVariantRecalibrator as SNPsVariantRecalibratorClassic { | ||
| input: | ||
| sites_only_variant_filtered_vcf = sites_only_variant_filtered_vcf, | ||
| sites_only_variant_filtered_vcf_index = sites_only_variant_filtered_vcf_idx, | ||
| recalibration_filename = base_name + ".snps.recal", | ||
| tranches_filename = base_name + ".snps.tranches", | ||
| recalibration_tranche_values = snp_recalibration_tranche_values, | ||
| recalibration_annotation_values = snp_recalibration_annotations, | ||
| hapmap_resource_vcf = hapmap_resource_vcf, | ||
| hapmap_resource_vcf_index = hapmap_resource_vcf_index, | ||
| omni_resource_vcf = omni_resource_vcf, | ||
| omni_resource_vcf_index = omni_resource_vcf_index, | ||
| one_thousand_genomes_resource_vcf = one_thousand_genomes_resource_vcf, | ||
| one_thousand_genomes_resource_vcf_index = one_thousand_genomes_resource_vcf_index, | ||
| dbsnp_resource_vcf = dbsnp_vcf, | ||
| dbsnp_resource_vcf_index = dbsnp_vcf_index, | ||
| use_allele_specific_annotations = true, | ||
| disk_size = "1000", | ||
| machine_mem_gb = SNP_VQSR_mem_gb_override, | ||
| max_gaussians = SNP_VQSR_max_gaussians_override, | ||
| } | ||
| } | ||
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| output { | ||
| File snps_variant_recalibration_file = select_first([MergeRecalibrationFiles.output_vcf, SNPsVariantRecalibratorClassic.recalibration]) | ||
| File snps_variant_recalibration_file_index = select_first([MergeRecalibrationFiles.output_vcf_index, SNPsVariantRecalibratorClassic.recalibration_index]) | ||
| File snps_variant_tranches_file = select_first([SNPGatherTranches.tranches_file, SNPsVariantRecalibratorClassic.tranches]) | ||
| File indels_variant_recalibration_file = IndelsVariantRecalibrator.recalibration | ||
| File indels_variant_recalibration_file_index = IndelsVariantRecalibrator.recalibration_index | ||
| File indels_variant_tranches_file = IndelsVariantRecalibrator.tranches | ||
| Array[File] monitoring_logs = select_all( | ||
| flatten( | ||
| [ | ||
| [IndelsVariantRecalibrator.monitoring_log], | ||
| [SNPsVariantRecalibratorCreateModel.monitoring_log], | ||
| select_first([SNPsVariantRecalibratorScattered.monitoring_log, []]), | ||
| [SNPGatherTranches.monitoring_log], | ||
| [MergeRecalibrationFiles.monitoring_log], | ||
| [SNPsVariantRecalibratorClassic.monitoring_log] | ||
| ])) | ||
| } | ||
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| } | ||
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nit: since these are being hard-coded, maybe don't even pass them as inputs, just have them hard-coded in the task?
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Yeah - I like that. It wasn't really clear to me why these were parameterized. It would seem unlikely that we would change this sort of thing.