Analysis Manifest JSON
To set up the analysisManifest.json to use in the CLI, use the following structure.
{
"libraryType": "<wgs>" or "<wes>",
"analysisFiles": <Analysis files. See Analysis Files>,
"analysisType": "rugd",
"dragenVersion": "<DRAGEN software version>",
"genomeReference": "<Reference genome>",
"notes": {"additional":"notes"},
"pedigree": [<Pedigree files. See Pedigree>],
"pedigreeName": "<Pedigree ID>"
}
To specify the location of analysis and metrics files, use the analysisFiles configuration in the analysisManifest.json. The following example specifies files in the specified storage container.
If libraryType is set to wes then "targetedRegionsBedFile": "<targeted regions>.bed.gz" is required.
"analysisFiles": {
"targetedRegionsBedFile": "<targeted regions>.bed.gz" (Not used if libraryType is set to wgs).
"jointFiles": <Pedigree data files. See Joint Files>,
"sampleFiles": <Sample files. See Sample Files>,
"referenceTar": "<Genome reference file>.tar",
"graphExpansionDependencies": <Reference files for STR plots. See Graph-Expansion Files"
}
Joint files include multi-sample VCFs and metrics files generated from the DRAGEN joint genotyping pipeline. At least one joint VCF file is required.
To specify the location of joint files, use the jointFiles configuration in the analysisManifest.json. The following example specifies the location of joint genotyping files.
"jointFiles": {
"jointCnvVcf": "<pedigreeName>.cnv.vcf.gz",
"jointRepeatsVcf": "<pedigreeName>.repeats.merged.vcf.gz",
"jointSnvVcf": "<pedigreeName>.snv.vcf.gz",
"jointSvVcf": "<pedigreeName>.sv.vcf.gz",
"metricsFiles": [
"<pedigreeName>.<metricInfo>_metrics.csv",
]
},
To enable coverage and callability metrics, include both the coverageReportBed and the callabilityReportBed output files. For more information, see Coverage/Callability Reports Use Cases and Expected Output .
DRAGEN produces pipeline-specific metrics reports during each run. Illumina recommends using the version of the files generated from map-align.
If using DRAGEN 3.9.5 analysis with SMN calling enabled then "smnTsv": "<Sample ID>.smn.tsv" is required.
"sampleFiles": {
"<SampleID>": {
"smnTsv": "<Sample ID>.smn.tsv" (Required if SMN is enabled with DRAGEN 3.9.6.
"alignments": "<SampleID>.bam",
"rohBed": "<SampleID>.roh.bed",
"bafBw": "<SampleID>.hard-filtered.baf.bw",
"targetCountsCorrected": "<SampleID>.target.counts.gc-corrected.gz",
"coverageReportBed": "<SampleID>.qc-coverage-region-1_cov_report.bed",
"callabilityReportBed": "<SampleID>.qc-coverage-region-1_callability.bed",
"repeatsData": {
"bam": "<SampleID>.repeats.bam",
"vcf": "<SampleID>.repeats.vcf.gz"
},
"metricsFiles": [
"<SampleID>.cnv_metrics.csv",
"<SampleID>.fastqc_metrics.csv",
"<SampleID>.gc_metrics.csv",
"<SampleID>.mapping_metrics.csv",
"<SampleID>.ploidy_estimation_metrics.csv",
"<SampleID>.qc-coverage-region-1_coverage_metrics.csv",
"<SampleID>.roh_metrics.csv",
"<SampleID>.trimmer_metrics.csv",
"<SampleID>.vc_metrics.csv",
"<SampleID>.wgs_coverage_metrics.csv"
]
},
To specify the location of input files used for generating STR plots, use the graphExpansionDependencies configuration in the analysisManifest.json. The following example specifies DRAGEN files.
"graphExpansionDependencies": {
"genomeFastaUrl": "<URL to the FASTA reference file>",
"smnRepeatSpecLink": "<URL to the repeat call specification file>"
},
To specify pedigree metadata, use the pedigree configuration in the analysisManifest.json.
"pedigree": [{
"id": "<Sample ID>",
"isAffected": "<Subject affected status>",
"maternalId": "<Maternal subject sample ID>",
"paternalId": "<Paternal subject sample ID>",
"sex": "<The sex of the sample subject>"
]}
Required Inputs for Interpretation
In cases that start from analysis results, interpretation functions are determined by the sample or joint files in the analysis manifest.
The following table lists the interpretation functions and required analysis files. If a required file is omitted, the associated variant filters, genetic findings, or IGV tracks are not functional.
|
Interpretation Function |
Required Analysis File Input |
TruSight Software Output File |
|---|---|---|
|
IGV B-allele bedgraph tracks |
<sampleID>.hard-filtered.baf.bw |
<sampleID>.baf.bedgraph.gz <sampleID>.baf.bedgraph.gz.tbi |
|
IGV BAM tracks |
<sampleID>.bam <sampleID>.bam.bai |
No output file |
|
IGV CNV GFF3 tracks |
<dragen-joint or single sample VCF>.cnv.vcf.gz <dragen-joint or single sample VCF>.cnv.vcf.gz.tbi |
CNV.<sampleID>.gff3 |
|
IGV Normalized coverage bedgraph tracks |
<sampleID>.target.counts.gc-corrected |
<sampleID>.counts.gc-corrected.bedgraph.gz <sampleID>.counts.gc-corrected.bedgraph.gz.tbi |
|
IGV ROH BED tracks |
<sampleID>.roh.bed |
No output file |
|
IGV single sample small variant VCF tracks |
<dragen-joint or single sample VCF>.hard-filtered.vcf.gz <dragen-joint or single sample VCF>.hard-filtered.vcf.gz.tbi |
<sampleID>.snv.vcf.gz <sampleID>.snv.vcf.gz.tbi |
|
IGV SV GFF3 tracks |
<dragen-joint or single sample VCF>.sv.vcf.gz <dragen-joint or single sample VCF>.sv.vcf.gz.tbi |
SV.<sampleID>.gff3 |
|
IGV Whole Genome Normalized coverage seg tracks |
<sampleID>.target.counts.gc-corrected |
<sampleID>.counts.gc-corrected.seg.gz |
|
IGV Whole Genome view B-allele seg tracks |
<sampleID>.baf.bedgraph.gz <sampleID>.target.counts.gc-corrected |
<sampleID>.baf.seg.gz |
|
Interpretation Coverage and Callability Filtering |
<sample ID>.qc-coverage-region-1_callability.bed <sample ID>.qc-coverage-region-1_cov_report.bed |
<sample ID>.callability.bed.gz <sample ID>.full-callability-report.bed.gz <sample ID>.coverage.bed.gz <sample ID>.full-coverage-report.bed.gz |
|
Interpretation SMN genetic findings |
<dragen-joint or single sample VCF>.repeats.vcf.gz <dragen-joint or single sample VCF>.repeats.vcf.gz.tbi Manifest Section: Graph Expansion Dependencies <sampleID>.smn.tsv |
No output file |
|
Interpretation STR genetic findings |
<dragen-joint or single sample VCF>.repeats.vcf.gz <dragen-joint or single sample VCF>.repeats.vcf.gz.tbi <sampleID>.repeats.bam <sampleID>.repeats.bam.bai Manifest Section: Graph Expansion Dependencies |
No output file |
|
Interpretation STR plots in Variant Details |
<dragen-joint or single sample VCF>.repeats.vcf.gz <dragen-joint or single sample VCF>.repeats.vcf.gz.tbi <sampleID>.repeats.bam <sampleID>.repeats.bam.bai |
No output file |
|
Interpretation with CNVs |
<dragen-joint or single sample VCF>.cnv.vcf.gz <dragen-joint or single sample VCF>.cnv.vcf.gz.tbi |
No output file |
|
Interpretation with ROH variants |
<sampleID>.roh.bed |
<sampleID>.roh.vcf.gz <sampleID>.roh.vcf.gz.tbi |
|
Interpretation with small variants |
<dragen-joint or single sample VCF>.hard-filtered.vcf.gz <dragen-joint or single sample VCF>.hard-filtered.vcf.gz.tbi
|
<caseID>.smn_dedup.vcf.gz <caseID>.smn_dedupvcf.gz.tbi
|
|
Interpretation with STRs |
<dragen-joint or single sample VCF>.repeats.vcf.gz <dragen-joint or single sample VCF>.repeats.vcf.gz.tbi |
No output file |
|
Interpretation with SVs |
<dragen-joint or single sample VCF>.sv.vcf.gz <dragen-joint or single sample VCF>.sv.vcf.gz.tbi |
<caseID>.indel_dedup.vcf.gz <caseID>.indel_dedup.vcf.gz.tbi |
Example JSON file
The following is an example analysisManifest.json file.
{
"analysisFiles": {
"graphExpansionDependencies": {
"genomeFastaUrl": "https://s3.amazonaws.com/stratus-documentation-us-east-1-public/dragen/reference/Homo_sapiens/hg38_alt_aware_nohla.fa",
"smnRepeatSpecLink": "gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-map-align/repeat-spec.json"
},
"jointFiles": {
"additionalVcfs": null,
"jointCnvVcf": "gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/joint-variants/cnv/16833908-d5b1-4df1-aea3-2995e0d856a3.cnv.vcf.gz",
"jointRepeatsVcf": "gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/joint-variants/repeats/16833908-d5b1-4df1-aea3-2995e0d856a3.repeats.merged.vcf.gz",
"jointSnvVcf": "gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/joint-variants/snv/16833908-d5b1-4df1-aea3-2995e0d856a3.hard-filtered.vcf.gz",
"jointSvVcf": "gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/sv/16833908-d5b1-4df1-aea3-2995e0d856a3.sv.vcf.gz",
"metricsFiles": [
"gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/joint-variants/cnv/16833908-d5b1-4df1-aea3-2995e0d856a3.cnv_metrics.csv",
"gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/joint-variants/snv/16833908-d5b1-4df1-aea3-2995e0d856a3.vc_metrics.csv",
"gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/sv/16833908-d5b1-4df1-aea3-2995e0d856a3.sv_metrics.csv"
]
},
"libraryType": "WGS",
"referenceTar": "https://use1-prd-seq-hub-appdata.s3.amazonaws.com/Edico_v8/hg38_altaware_nohla-cnv-anchored.v8.tar",
"sampleFiles": {
"123IT_9phBz4w8": {
"alignments": "gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-map-align/123IT_9phBz4w8.bam",
"bafBw": "gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-small-variants/123IT_9phBz4w8.hard-filtered.baf.bw",
"callabilityReportBed": "gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-small-variants/123IT_9phBz4w8.qc-coverage-region-1_callability.bed",
"coverageReportBed": "gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-small-variants/123IT_9phBz4w8.qc-coverage-region-1_cov_report.bed",
"metricsFiles": [
"gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-map-align/123IT_9phBz4w8.fastqc_metrics.csv",
"gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-map-align/123IT_9phBz4w8.trimmer_metrics.csv",
"gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-map-align/123IT_9phBz4w8.gc_metrics.csv",
"gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-map-align/123IT_9phBz4w8.mapping_metrics.csv",
"gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-map-align/123IT_9phBz4w8.ploidy_estimation_metrics.csv",
"gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-map-align/123IT_9phBz4w8.wgs_coverage_metrics.csv",
"gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-small-variants/123IT_9phBz4w8.vc_metrics.csv",
"gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-small-variants/123IT_9phBz4w8.cnv_metrics.csv",
"gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-small-variants/123IT_9phBz4w8.qc-coverage-region-1_coverage_metrics.csv",
"gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-small-variants/123IT_9phBz4w8.roh_metrics.csv"
],
"repeatsData": {
"bam": "gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-map-align/123IT_9phBz4w8.repeats.bam",
"vcf": "gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-map-align/123IT_9phBz4w8.repeats.vcf.gz"
},
"rohBed": "gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-small-variants/123IT_9phBz4w8.roh.bed",
"smnTsv": "gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-small-variants/123IT_9phBz4w8.smn.tsv",
"targetCountsCorrected": "gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/123IT_9phBz4w8-small-variants/123IT_9phBz4w8.target.counts.gc-corrected.gz"
},
"2242Ou66NKA_Y8": {
"alignments": "gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/2242Ou66NKA_Y8-map-align/2242Ou66NKA_Y8.bam",
"bafBw": "gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/2242Ou66NKA_Y8-small-variants/2242Ou66NKA_Y8.hard-filtered.baf.bw",
"callabilityReportBed": "gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/2242Ou66NKA_Y8-small-variants/2242Ou66NKA_Y8.qc-coverage-region-1_callability.bed",
"coverageReportBed": "gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/2242Ou66NKA_Y8-small-variants/2242Ou66NKA_Y8.qc-coverage-region-1_cov_report.bed",
"metricsFiles": [
"gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/2242Ou66NKA_Y8-map-align/2242Ou66NKA_Y8.fastqc_metrics.csv",
"gds://wgs-c336a77b-23a9-4d18-96f8-aa1e371e330e/f8cf9bbd-a7f5-366e-9861-b30d14efe1f7/cases/16833908-d5b1-4df1-aea3-2995e0d856a3/fwe.819eece572214a9a81bff3d2cc9cef01/2242Ou66NKA_Y8-map-align/2242Ou66NKA_Y8.trimmer_metrics.csv",
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