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Dev #47

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merged 28 commits into from
Jan 13, 2020
Merged

Dev #47

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733d7e5
Updated to gatk4.1, Update VariantRecal syntax
Feb 22, 2019
3f5f6e8
Merge branch 'master' of github.com:gatk-workflows/gatk4-germline-snp…
Feb 22, 2019
fe77d80
added samtools path variable
Feb 22, 2019
dd632f0
Updated wording
Feb 23, 2019
bff1267
add a version of joint-discovery that takes in an array for gvcfs
Feb 24, 2019
082df3b
Update README.md
Feb 28, 2019
05ce4ef
Merge branch 'master' into dev
Feb 28, 2019
093e478
increased mem for SNPsVariantRecalibrator for papiv2
May 3, 2019
329f152
increased mem for SNPsVariantRecalibrator for papiv2
May 3, 2019
7184b70
increased memory to run on papiv2
May 6, 2019
6304e56
correction to variable names in json
Jul 16, 2019
447d0b7
Merge branch 'master' into dev
Oct 30, 2019
411c494
corrected parameter syntax for SNPsVariantRecalibrator task
Oct 30, 2019
37b019e
Merge branch 'master' of github.com:gatk-workflows/gatk4-germline-snp…
Oct 31, 2019
043e443
Updated haplotypecaller to WDL 1.0, removed comments from haplotypeca…
Nov 1, 2019
c4ce8f6
Added WDL 1.0 version of JointGenotyping to soon replace joint discov…
Nov 1, 2019
e189a70
Update genotype2develop (#44)
Dec 2, 2019
0e2d9c2
Update genotype2develop (#45)
Dec 2, 2019
481a177
Update genotype2develop (#46)
Dec 2, 2019
c61c128
Update genotype2develop (#48)
Dec 3, 2019
cd1b265
removed unnecessary optional override variables
Dec 6, 2019
7da5824
replaced '$' with '~'
Dec 18, 2019
976988f
updated broad reference bucket path
Jan 8, 2020
30d95c1
Add important notes regarding JointGenotype workflow to Readme
Jan 9, 2020
dae5566
minor update to Readme, renamed input file name in json
Jan 9, 2020
87b6198
minor spelling
Jan 9, 2020
3416bbd
Added allele-specific annotations to HC command
Jan 13, 2020
fec5975
Updated import url to the next release tag
Jan 13, 2020
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574 changes: 574 additions & 0 deletions JointGenotyping-terra.wdl
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41 changes: 41 additions & 0 deletions JointGenotyping.hg19.wgs.inputs.json
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{
"JointGenotyping.sample_name_map": "gs://gatk-test-data/1kgp/downsampled_gvcf_hg37/hg37.1kg_50.sample_map",
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"JointGenotyping.callset_name": "NA12878",
"JointGenotyping.unbounded_scatter_count_scale_factor": 2.5,
"JointGenotyping.SplitIntervalList.scatter_mode": "INTERVAL_SUBDIVISION",

"JointGenotyping.unpadded_intervals_file": "gs://gatk-test-data/intervals/wgs_calling_regions.v1.list",
"JointGenotyping.ref_fasta": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta",
"JointGenotyping.ref_fasta_index": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.fasta.fai",
"JointGenotyping.ref_dict": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.dict",
"JointGenotyping.eval_interval_list": "gs://gcp-public-data--broad-references/hg19/v0/wgs_evaluation_regions.v1.interval_list",
"JointGenotyping.haplotype_database": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.haplotype_database.txt",

"JointGenotyping.axiomPoly_resource_vcf": "gs://gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz",
"JointGenotyping.axiomPoly_resource_vcf_index": "gs://gcp-public-data--broad-references/hg19/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.vcf.gz.tbi",
"JointGenotyping.dbsnp_vcf": "gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz",
"JointGenotyping.dbsnp_vcf_index": "gs://gcp-public-data--broad-references/hg19/v0/dbsnp_138.b37.vcf.gz.tbi",
"JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg19/v0/hapmap_3.3.b37.vcf.gz",
"JointGenotyping.hapmap_resource_vcf_index": "gs://gcp-public-data--broad-references/hg19/v0/hapmap_3.3.b37.vcf.gz.tbi",
"JointGenotyping.mills_resource_vcf": "gs://gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf",
"JointGenotyping.mills_resource_vcf_index": "gs://gcp-public-data--broad-references/hg19/v0/Mills_and_1000G_gold_standard.indels.b37.sites.vcf.idx",
"JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg19/v0/1000G_omni2.5.b37.vcf.gz",
"JointGenotyping.omni_resource_vcf_index": "gs://gcp-public-data--broad-references/hg19/v0/1000G_omni2.5.b37.vcf.gz.tbi",
"JointGenotyping.one_thousand_genomes_resource_vcf": "gs://gcp-public-data--broad-references/hg19/v0/1000G_phase1.snps.high_confidence.b37.vcf.gz",
"JointGenotyping.one_thousand_genomes_resource_vcf_index": "gs://gcp-public-data--broad-references/hg19/v0/1000G_phase1.snps.high_confidence.b37.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
}
35 changes: 35 additions & 0 deletions JointGenotyping.hg38.terra.wgs.inputs.json
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{
"JointGenotyping.large_disk":"1000",
"JointGenotyping.medium_disk":"200",
"JointGenotyping.indel_recalibration_annotation_values":["FS","ReadPosRankSum","MQRankSum","QD","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.unbounded_scatter_count_scale_factor":"2.5",
"JointGenotyping.omni_resource_vcf_index":"gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz.tbi",
"JointGenotyping.eval_interval_list":"gs://gcp-public-data--broad-references/hg38/v0/wgs_evaluation_regions.hg38.interval_list",
"JointGenotyping.one_thousand_genomes_resource_vcf_index":"gs://gcp-public-data--broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi",
"JointGenotyping.one_thousand_genomes_resource_vcf":"gs://gcp-public-data--broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"JointGenotyping.small_disk":"100",
"JointGenotyping.snp_recalibration_annotation_values":"[QD,MQRankSum,ReadPosRankSum,FS,MQ,SOR,DP]",
"JointGenotyping.dbsnp_vcf":"gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf",
"JointGenotyping.callset_name":"hg38_1kg_50",
"JointGenotyping.unpadded_intervals_file":"gs://gcp-public-data--broad-references/hg38/v0/hg38.even.handcurated.20k.intervals",
"JointGenotyping.dbsnp_vcf_index":"gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
"JointGenotyping.ref_fasta_index":"gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"JointGenotyping.ref_dict":"gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
"JointGenotyping.mills_resource_vcf_index":"gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
"JointGenotyping.sample_name_map":"gs://gatk-test-data/joint_discovery/1kg_50_hg38/gvcf/hg38_1kg_50.sample_map",
"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.omni_resource_vcf":"gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
"JointGenotyping.mills_resource_vcf":"gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"JointGenotyping.axiomPoly_resource_vcf":"gs://gcp-public-data--broad-references/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz",
"JointGenotyping.snp_filter_level":"99.7",
"JointGenotyping.snps_variant_recalibration_threshold":"20000",
"JointGenotyping.haplotype_database":"gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
"JointGenotyping.hapmap_resource_vcf":"gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.indel_filter_level":"99",
"JointGenotyping.axiomPoly_resource_vcf_index":"gs://gcp-public-data--broad-references/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi",
"JointGenotyping.ref_fasta":"gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
"JointGenotyping.hapmap_resource_vcf_index":"gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz.tbi",
"JointGenotyping.SNP_VQSR_downsampleFactor":"10",
"JointGenotyping.huge_disk":"2000"
}
41 changes: 41 additions & 0 deletions JointGenotyping.hg38.wgs.inputs.json
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{
"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://gcp-public-data--broad-references/hg38/v0/hg38.even.handcurated.20k.intervals",
"JointGenotyping.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
"JointGenotyping.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"JointGenotyping.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
"JointGenotyping.eval_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/wgs_evaluation_regions.hg38.interval_list",
"JointGenotyping.haplotype_database": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",

"JointGenotyping.axiomPoly_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz",
"JointGenotyping.axiomPoly_resource_vcf_index": "gs://gcp-public-data--broad-references/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi",
"JointGenotyping.dbsnp_vcf": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf",
"JointGenotyping.dbsnp_vcf_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
"JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.hapmap_resource_vcf_index": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz.tbi",
"JointGenotyping.mills_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"JointGenotyping.mills_resource_vcf_index": "gs://gcp-public-data--broad-references/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
"JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf_index": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz.tbi",
"JointGenotyping.one_thousand_genomes_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"JointGenotyping.one_thousand_genomes_resource_vcf_index": "gs://gcp-public-data--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
}
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