-
Notifications
You must be signed in to change notification settings - Fork 1
/
Multisample_jointgt_GATK4_inputs_hg38.json
38 lines (33 loc) · 3.09 KB
/
Multisample_jointgt_GATK4_inputs_hg38.json
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
{{
"##_COMMENT1": "INPUT GVCFs & COHORT -- DATASET-SPECIFC, MUST BE ADAPTED. CALLSET NAME IS THE PREFIX FOR YOUR FINAL OUTPUT FILES",
"JointGenotyping.sample_sheet": "gvcfs.txt",
"JointGenotyping.callset_name": "wgs_hg38",
"##_COMMENT2": "REFERENCE FILES",
"JointGenotyping.ref_fasta": "/scratch/pawsey0001/sbeecroft/hg38/v0/Homo_sapiens_assembly38.fasta",
"JointGenotyping.ref_fasta_index": "/scratch/pawsey0001/sbeecroft/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"JointGenotyping.ref_dict": "/scratch/pawsey0001/sbeecroft/hg38/v0/Homo_sapiens_assembly38.dict",
"##_COMMENT3": "INTERVALS",
"JointGenotyping.eval_interval_list": "/scratch/pawsey0001/sbeecroft/hg38/v0/wgs_evaluation_regions.hg38.interval_list",
"JointGenotyping.unpadded_intervals_file": "/scratch/pawsey0001/sbeecroft/hg38/v0/hg38.custom_100Mb.intervals",
"##_COMMENT4": "RESOURCE FILES",
"JointGenotyping.dbsnp_vcf": "/scratch/pawsey0001/sbeecroft/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf",
"JointGenotyping.dbsnp_vcf_index": "/scratch/pawsey0001/sbeecroft/hg38/v0/Homo_sapiens_assembly38.dbsnp138.vcf.idx",
"JointGenotyping.one_thousand_genomes_resource_vcf": "/scratch/pawsey0001/sbeecroft/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz",
"JointGenotyping.one_thousand_genomes_resource_vcf_index": "/scratch/pawsey0001/sbeecroft/hg38/v0/1000G_phase1.snps.high_confidence.hg38.vcf.gz.tbi",
"JointGenotyping.omni_resource_vcf": "/scratch/pawsey0001/sbeecroft/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf_index": "/scratch/pawsey0001/sbeecroft/hg38/v0/1000G_omni2.5.hg38.vcf.gz.tbi",
"JointGenotyping.mills_resource_vcf": "/scratch/pawsey0001/sbeecroft/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
"JointGenotyping.mills_resource_vcf_index": "/scratch/pawsey0001/sbeecroft/hg38/v0/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
"JointGenotyping.axiomPoly_resource_vcf": "/scratch/pawsey0001/sbeecroft/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz",
"JointGenotyping.axiomPoly_resource_vcf_index": "/scratch/pawsey0001/sbeecroft/hg38/v0/Axiom_Exome_Plus.genotypes.all_populations.poly.hg38.vcf.gz.tbi",
"JointGenotyping.hapmap_resource_vcf": "/scratch/pawsey0001/sbeecroft/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.hapmap_resource_vcf_index": "/scratch/pawsey0001/sbeecroft/hg38/v0/hapmap_3.3.hg38.vcf.gz.tbi",
"##_COMMENT5": "VQSR PARAMETERS",
"JointGenotyping.SNP_VQSR_downsampleFactor": 10,
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.indel_filter_level": 99.7,
"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.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.snp_recalibration_annotation_values": ["QD", "MQRankSum", "ReadPosRankSum", "FS", "MQ", "SOR", "DP"]
}