Dev

JointGenotyping.hg38.wgs.inputs.json

@@ -0,0 +1,41 @@
+{
+  "JointGenotyping.sample_name_map": "gs://gatk-test-data/joint_discovery/1kg_50_hg38/gvcf/hg38_1kg_50.sample_map",
+  "JointGenotyping.callset_name": "hg38_1kg_50",
+  "JointGenotyping.unbounded_scatter_count_scale_factor": 2.5,
+  "JointGenotyping.SplitIntervalList.scatter_mode": "INTERVAL_SUBDIVISION",
+
+  "JointGenotyping.unpadded_intervals_file": "gs://broad-references/hg38/v0/hg38.even.handcurated.20k.intervals",
+  "JointGenotyping.ref_fasta": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
+  "JointGenotyping.ref_fasta_index": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
+  "JointGenotyping.ref_dict": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
+  "JointGenotyping.eval_interval_list": "gs://broad-references/hg38/v0/wgs_evaluation_regions.hg38.interval_list",
+  "JointGenotyping.haplotype_database": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
+
+  "JointGenotyping.axiomPoly_resource_vcf": "gs://broad-references/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz",
+  "JointGenotyping.axiomPoly_resource_vcf_index": "gs://broad-references/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi",
+  "JointGenotyping.dbsnp_vcf": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf",
+  "JointGenotyping.dbsnp_vcf_index": "gs://broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
+  "JointGenotyping.hapmap_resource_vcf": "gs://broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
+  "JointGenotyping.hapmap_resource_vcf_index": "gs://broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz.tbi",
+  "JointGenotyping.mills_resource_vcf": "gs://broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
+  "JointGenotyping.mills_resource_vcf_index": "gs://broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
+  "JointGenotyping.omni_resource_vcf": "gs://broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
+  "JointGenotyping.omni_resource_vcf_index": "gs://broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz.tbi",
+  "JointGenotyping.one_thousand_genomes_resource_vcf": "gs://broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
+  "JointGenotyping.one_thousand_genomes_resource_vcf_index": "gs://broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi",
+
+  "JointGenotyping.SNP_VQSR_downsampleFactor": 10,
+  "JointGenotyping.snps_variant_recalibration_threshold": 20000,
+  "JointGenotyping.snp_filter_level": 99.7,
+  "JointGenotyping.snp_recalibration_annotation_values": ["QD", "MQRankSum", "ReadPosRankSum", "FS", "MQ", "SOR", "DP"],
+  "JointGenotyping.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" ],
+
+  "JointGenotyping.indel_filter_level": 99.0,
+  "JointGenotyping.indel_recalibration_annotation_values": ["FS", "ReadPosRankSum", "MQRankSum", "QD", "SOR", "DP"],
+  "JointGenotyping.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"],
+
+  "JointGenotyping.small_disk": 100,
+  "JointGenotyping.medium_disk": 200,
+  "JointGenotyping.large_disk": 1000,
+  "JointGenotyping.huge_disk": 2000
+}

README.md

@@ -4,11 +4,16 @@
 Workflows for [germline short variant discovery](https://software.broadinstitute.org/gatk/best-practices/workflow?id=11145) with GATK4. 
 
 ### haplotypecaller-gvcf-gatk :
-The haplotypecaller-gvcf-gatk4 workflow runs the HaplotypeCaller tool
-from GATK4 in GVCF mode on a single sample according to GATK Best Practices. 
-When executed the workflow scatters the HaplotypeCaller tool over a sample 
-using an intervals list file. The output file produced will be a 
-single gvcf file which can be used by the joint-discovery workflow.
+The haplotypecaller-gvcf-gatk4 workflow runs the GATK4 HaplotypeCaller tool
+in GVCF mode on a single sample according to GATK Best Practices. When 
+executed the workflow scatters the HaplotypeCaller tool over the input bam sample 
+using an interval list file. The output produced by the workflow will be a single GVCF 
+file which can then be provided to the JointGenotyping workflow along with several other 
+GVCF files to call for variants simultaneously, producing a multisample VCF. 
+The haplotypecaller-gvcf-gatk4 workflows default GVCF mode is useful when calling variants 
+for several samples efficiently. However, for instances when calling variants for one or a 
+few samples it is possible to have the workflow directly call variants and output a VCF file by 
+setting the `make_gvcf` input variable to `false`. 
 
 #### Requirements/expectations
 - One analysis-ready BAM file for a single sample (as identified in RG:SM)
@@ -17,22 +22,22 @@ single gvcf file which can be used by the joint-discovery workflow.
 #### Outputs 
 - One GVCF file and its index
 
-### joint-discovery-gatk :
+### JointGenotyping.wdl :
 This WDL implements the joint calling and VQSR filtering portion of the 
 GATK Best Practices for germline SNP and Indel discovery 
-in human whole-genome sequencing (WGS).
+in human whole-genome sequencing (WGS). The workflow accept a sample map 
+file with 50 or more GVCFs and produces a multisample VCF.
 
 *NOTE:*  
-*- joint-discovery-gatk4-local.wdl is a slightly modified version of the 
-original to support users interested in running the workflow locally.*  
-*- joint-discovery-gatk4-fc.wdl is a slightly modified version of the 
-original to support users interested in running the workflow firecloud with and
-using an array of gvcfs as input.*
+*- JointGenotyping-terra.wdl is a slightly modified version of the 
+original workflow to support users interested in running the 
+workflow on Terra. The changes include variables for dockers and disksize, making 
+it easier to configure the workflow.*
 
 
 #### Requirements/expectations
 - One or more GVCFs produced by HaplotypeCaller in GVCF mode
-- Bare minimum 1 WGS sample or 30 Exome samples. Gene panels are not supported.
+- Bare minimum 50 samples. Gene panels are not supported.
 - When determining disk size in the JSON, use the guideline below
   - small_disk = (num_gvcfs / 10) + 10
   - medium_disk = (num_gvcfs * 15) + 10
@@ -45,7 +50,7 @@ using an array of gvcfs as input.*
   in the FILTER field.
 
 ### Software version requirements :
-- GATK 4.1 
+- GATK 4.1.4.0 
 - Samtools 1.3.1
 - Python 2.7
 - Cromwell version support