Updated the link to the Funcotator info/tutorial page. #6920
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jonn-smith
commented
Oct 28, 2020
•
jonn-smith
commented
- Creating PR for update to Funcotator documentation and to show off CARROT integration.
|
#carrot(HaplotypeCaller DRAGEN WGS1 revised 7, in_gatk_docker_override, in_dummy_docker_placeholder) |
Started a CARROT test run : HaplotypeCaller DRAGEN WGS1 revised 7_run_2020-10-29 01:05:55.379753448 UTC
{
"run_id": "e3422e8d-d2d8-48f2-b608-c51cbc762018",
"test_id": "bfab1ecf-024f-4c42-9b32-4e9a5d5643f8",
"name": "HaplotypeCaller DRAGEN WGS1 revised 7_run_2020-10-29 01:05:55.379753448 UTC",
"status": "building",
"test_input": {
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"in_dataset_name": "CH1_CHM13_WGS1_downsampled",
"in_dragstr_params": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/CHMI_CHMI3_WGS1_downsampled.gatk-dragstr-table.txt",
"in_enableBQD": "true",
"in_enableDRAGSTR": "true",
"in_enableDRDQ": "true",
"in_enableFRD": "true",
"in_evalLabel": "GATK",
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"in_hapMap": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
"in_input_bam": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/CHMI_CHMI3_WGS1_downsampled.bam",
"in_input_bam_index": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/CHMI_CHMI3_WGS1_downsampled.bam.bai",
"in_make_bamout": "true",
"in_make_gvcf": "false",
"in_preemptible": "0",
"in_refDict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
"in_refIndex": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"in_ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
"in_ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
"in_ref_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"in_reference": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
"in_referenceVersion": "hg38",
"in_scattered_calling_intervals_list": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/wgs_scattered_calling_intervals.txt",
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"in_truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/chm.full.m38.vcf.gz.tbi",
"in_vcfScoreField": "QUAL"
},
"eval_input": {
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"in_sample2_indel_LCR_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_LCR_vcfeval_non_snp_roc.tsv.gz",
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"in_sample2_snp_HCR_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_HCR_vcfeval_snp_roc.tsv.gz",
"in_sample2_snp_LCR_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_LCR_vcfeval_snp_roc.tsv.gz",
"in_sample2_snp_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_vcfeval_snp_roc.tsv.gz"
},
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"created_at": "2020-10-29T01:05:55.379830",
"created_by": null,
"finished_at": null
}
|
CARROT test run finished
{
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"test_id": "bfab1ecf-024f-4c42-9b32-4e9a5d5643f8",
"name": "HaplotypeCaller DRAGEN WGS1 revised 7_run_2020-10-29 01:02:53.874008692 UTC",
"status": "failed",
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"in_input_bam_index": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/CHMI_CHMI3_WGS1_downsampled.bam.bai",
"in_make_bamout": "true",
"in_make_gvcf": "false",
"in_preemptible": "0",
"in_refDict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
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"in_ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
"in_ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
"in_ref_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"in_reference": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
"in_referenceVersion": "hg38",
"in_scattered_calling_intervals_list": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/wgs_scattered_calling_intervals.txt",
"in_stratIntervals": [
"gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/LCR_Hg38.interval_list",
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],
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"LCR",
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"in_truthVcf": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/chm.full.m38.vcf.gz",
"in_truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/chm.full.m38.vcf.gz.tbi",
"in_vcfScoreField": "QUAL"
},
"eval_input": {
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"in_eval_dataset_name": "CHMI_CHMI3_WGS1_downsampled",
"in_sample2_indel_HCR_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_HCR_vcfeval_non_snp_roc.tsv.gz",
"in_sample2_indel_LCR_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_LCR_vcfeval_non_snp_roc.tsv.gz",
"in_sample2_indel_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_vcfeval_non_snp_roc.tsv.gz",
"in_sample2_snp_HCR_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_HCR_vcfeval_snp_roc.tsv.gz",
"in_sample2_snp_LCR_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_LCR_vcfeval_snp_roc.tsv.gz",
"in_sample2_snp_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_vcfeval_snp_roc.tsv.gz"
},
"cromwell_job_id": "b351f14e-24cf-48c8-a42e-8a49f51b767d",
"created_at": "2020-10-29T01:02:53.874057",
"created_by": null,
"finished_at": "2020-10-29T08:31:22.364",
"results": null
}
|
|
#carrot(HaplotypeCaller DRAGEN WGS1 revised 8, in_gatk_docker_override, in_dummy_docker_placeholder) |
Started a CARROT test run : HaplotypeCaller DRAGEN WGS1 revised 8_run_2020-10-29 12:00:54.299420663 UTC
{
"run_id": "1cb48356-6b1e-467f-8f58-2007ed2bffb3",
"test_id": "8003518b-70d4-495a-8b84-e91ef320647f",
"name": "HaplotypeCaller DRAGEN WGS1 revised 8_run_2020-10-29 12:00:54.299420663 UTC",
"status": "building",
"test_input": {
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"in_dataset_name": "CH1_CHM13_WGS1_downsampled",
"in_dragstr_params": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/CHMI_CHMI3_WGS1_downsampled.gatk-dragstr-table.txt",
"in_enableBQD": "true",
"in_enableDRAGSTR": "true",
"in_enableDRDQ": "true",
"in_enableFRD": "true",
"in_evalLabel": "GATK",
"in_gatk_docker_override": "image_build:gatk|d060380d5e76d367bf631e49d931cafd17a3d42a",
"in_hapMap": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
"in_input_bam": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/CHMI_CHMI3_WGS1_downsampled.bam",
"in_input_bam_index": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/CHMI_CHMI3_WGS1_downsampled.bam.bai",
"in_make_bamout": "true",
"in_make_gvcf": "false",
"in_preemptible": "0",
"in_refDict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
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"in_ref_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
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"in_referenceVersion": "hg38",
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],
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"in_vcfScoreField": "QUAL"
},
"eval_input": {
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"in_sample2_indel_HCR_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_HCR_vcfeval_non_snp_roc.tsv.gz",
"in_sample2_indel_LCR_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_LCR_vcfeval_non_snp_roc.tsv.gz",
"in_sample2_indel_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_vcfeval_non_snp_roc.tsv.gz",
"in_sample2_snp_HCR_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_HCR_vcfeval_snp_roc.tsv.gz",
"in_sample2_snp_LCR_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_LCR_vcfeval_snp_roc.tsv.gz",
"in_sample2_snp_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_vcfeval_snp_roc.tsv.gz"
},
"cromwell_job_id": null,
"created_at": "2020-10-29T12:00:54.299503",
"created_by": null,
"finished_at": null
}
|
CARROT test run finished
{
"run_id": "1cb48356-6b1e-467f-8f58-2007ed2bffb3",
"test_id": "8003518b-70d4-495a-8b84-e91ef320647f",
"name": "HaplotypeCaller DRAGEN WGS1 revised 8_run_2020-10-29 12:00:54.299420663 UTC",
"status": "succeeded",
"test_input": {
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"in_dataset_name": "CH1_CHM13_WGS1_downsampled",
"in_dragstr_params": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/CHMI_CHMI3_WGS1_downsampled.gatk-dragstr-table.txt",
"in_enableBQD": "true",
"in_enableDRAGSTR": "true",
"in_enableDRDQ": "true",
"in_enableFRD": "true",
"in_evalLabel": "GATK",
"in_gatk_docker_override": "image_build:gatk|d060380d5e76d367bf631e49d931cafd17a3d42a",
"in_hapMap": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.haplotype_database.txt",
"in_input_bam": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/CHMI_CHMI3_WGS1_downsampled.bam",
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"in_make_bamout": "true",
"in_make_gvcf": "false",
"in_preemptible": "0",
"in_refDict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
"in_refIndex": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"in_ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
"in_ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
"in_ref_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"in_reference": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
"in_referenceVersion": "hg38",
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"gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/LCR_Hg38.interval_list",
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],
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"LCR",
"HCR"
],
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"in_truthVcf": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/chm.full.m38.vcf.gz",
"in_truthVcfIndex": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/chm.full.m38.vcf.gz.tbi",
"in_vcfScoreField": "QUAL"
},
"eval_input": {
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"in_eval_dataset_name": "CHMI_CHMI3_WGS1_downsampled",
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"in_sample2_indel_LCR_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_LCR_vcfeval_non_snp_roc.tsv.gz",
"in_sample2_indel_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_vcfeval_non_snp_roc.tsv.gz",
"in_sample2_snp_HCR_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_HCR_vcfeval_snp_roc.tsv.gz",
"in_sample2_snp_LCR_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_LCR_vcfeval_snp_roc.tsv.gz",
"in_sample2_snp_roc_table": "gs://dsp-methods-carrot-data/test_data/Dragen_GATK_Concordance/cached_dragen_sample_data/CHMI_CHMI3_WGS1_downsampled_DRAGEN_dragen_chm_vcfeval_snp_roc.tsv.gz"
},
"cromwell_job_id": "f3e6a562-43c4-48ac-b815-c47cb8822d08",
"created_at": "2020-10-29T12:00:54.299503",
"created_by": null,
"finished_at": "2020-10-29T12:23:13.037",
"results": {
"F Score": "gs://broad-dsde-methods-carrot-cromwell/merged_workflow/f3e6a562-43c4-48ac-b815-c47cb8822d08/call-call_eval/eval.HC_Dragen_eval/8fa3d5d9-c21b-411e-a229-3bb06bc1c729/call-Plot/CHMI_CHMI3_WGS1_downsampled_best_fscore.tsv",
"ROC Curve Image": "gs://broad-dsde-methods-carrot-cromwell/merged_workflow/f3e6a562-43c4-48ac-b815-c47cb8822d08/call-call_eval/eval.HC_Dragen_eval/8fa3d5d9-c21b-411e-a229-3bb06bc1c729/call-Plot/CHMI_CHMI3_WGS1_downsampled_snp.png",
"TSV": "gs://broad-dsde-methods-carrot-cromwell/merged_workflow/f3e6a562-43c4-48ac-b815-c47cb8822d08/call-call_eval/eval.HC_Dragen_eval/8fa3d5d9-c21b-411e-a229-3bb06bc1c729/call-Plot/CHMI_CHMI3_WGS1_downsampled.tsv"
}
}
|
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