Merge pull request broadinstitute#415 from broadinstitute/gg_GL-1594_…

…ChangeArraysHapMapConcordanceThresholdTo95 GL-1594. Change default threshold to pass Hapmap control genotype concordance
kew24 · Sep 9, 2021 · 6423592 · 6423592
2 parents 28bd37c + f3793ba
commit 6423592
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diff --git a/pipelines/broad/arrays/single_sample/Arrays.changelog.md b/pipelines/broad/arrays/single_sample/Arrays.changelog.md
@@ -1,11 +1,8 @@
-# 2.4.2
-2021-09-07
-
-* Modified pipeline to automatically generate the analysis_version_number if it is not supplied as an input.
-
 # 2.4.1
-2021-08-30
+2021-09-09
 
+* Changed default threshold for passing control (HapMap) genotype concordance from 0.98 to 0.95
+* Modified pipeline to automatically generate the analysis_version_number if it is not supplied as an input.
 * Modified pipeline to make several inputs optional:
     * sample_id
     * participant_id

diff --git a/pipelines/broad/arrays/single_sample/Arrays.wdl b/pipelines/broad/arrays/single_sample/Arrays.wdl
@@ -22,7 +22,7 @@ import "../../../../tasks/broad/InternalTasks.wdl" as InternalTasks
 
 workflow Arrays {
 
-  String pipeline_version = "2.4.2"
+  String pipeline_version = "2.4.1"
 
   input {
 
@@ -41,7 +41,7 @@ workflow Arrays {
     String? participant_id
 
     Float call_rate_threshold = 0.98
-    Float genotype_concordance_threshold = 0.98
+    Float genotype_concordance_threshold = 0.95
 
     File red_idat_cloud_path
     File green_idat_cloud_path

diff --git a/pipelines/broad/arrays/single_sample/ExampleWorkflow.inputs.json b/pipelines/broad/arrays/single_sample/ExampleWorkflow.inputs.json
@@ -3,7 +3,6 @@
   "Arrays.sample_lsid": "broadinstitute.org:bsp.dev.sample:NOTREAL.NA12878",
   "Arrays.analysis_version_number": 1,
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
   "Arrays.reported_gender": "Female",
   "Arrays.chip_well_barcode": "7991775143_R01C01",
 

diff --git a/pipelines/broad/arrays/single_sample/test_inputs/Plumbing/SimpleInput.json b/pipelines/broad/arrays/single_sample/test_inputs/Plumbing/SimpleInput.json
@@ -19,7 +19,6 @@
   "Arrays.research_project_id": "RP-45",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/HumanExome-12v1-1_A/idats/7991775143_R01C01/7991775143_R01C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/HumanExome-12v1-1_A/idats/7991775143_R01C01/7991775143_R01C01_Red.idat",

diff --git a/pipelines/broad/arrays/single_sample/test_inputs/Scientific/101342370027_R02C01_NA12878.json b/pipelines/broad/arrays/single_sample/test_inputs/Scientific/101342370027_R02C01_NA12878.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-1014",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/PsychChip_v1-1_15073391_A1/idats/101342370027_R02C01/101342370027_R02C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/PsychChip_v1-1_15073391_A1/idats/101342370027_R02C01/101342370027_R02C01_Red.idat",

diff --git a/pipelines/broad/arrays/single_sample/test_inputs/Scientific/101342370027_R12C02_NA12892.json b/pipelines/broad/arrays/single_sample/test_inputs/Scientific/101342370027_R12C02_NA12892.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-1014",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/PsychChip_v1-1_15073391_A1/idats/101342370027_R12C02/101342370027_R12C02_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/PsychChip_v1-1_15073391_A1/idats/101342370027_R12C02/101342370027_R12C02_Red.idat",

diff --git a/pipelines/broad/arrays/single_sample/test_inputs/Scientific/101342370134_R12C02_NA12891.json b/pipelines/broad/arrays/single_sample/test_inputs/Scientific/101342370134_R12C02_NA12891.json
@@ -11,7 +11,6 @@
   "Arrays.research_project_id": "RP-1014",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/PsychChip_v1-1_15073391_A1/idats/101342370134_R12C02/101342370134_R12C02_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/PsychChip_v1-1_15073391_A1/idats/101342370134_R12C02/101342370134_R12C02_Red.idat",

diff --git a/pipelines/broad/arrays/single_sample/test_inputs/Scientific/200246060179_R09C02_NA12878.json b/pipelines/broad/arrays/single_sample/test_inputs/Scientific/200246060179_R09C02_NA12878.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-30",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumImmunoArray-24v2-0_A/idats/200246060179_R09C02/200246060179_R09C02_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumImmunoArray-24v2-0_A/idats/200246060179_R09C02/200246060179_R09C02_Red.idat",

diff --git a/...nes/broad/arrays/single_sample/test_inputs/Scientific/200557060038_R10C02_PRISM_7032.json b/...nes/broad/arrays/single_sample/test_inputs/Scientific/200557060038_R10C02_PRISM_7032.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-30",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Broad_GWAS_supplemental_15061359_A1/idats/200557060038_R10C02/200557060038_R10C02_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Broad_GWAS_supplemental_15061359_A1/idats/200557060038_R10C02/200557060038_R10C02_Red.idat",

diff --git a/...ingle_sample/test_inputs/Scientific/200557060038_R10C02_PRISM_7032_PullFPFromMercury.json b/...ingle_sample/test_inputs/Scientific/200557060038_R10C02_PRISM_7032_PullFPFromMercury.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-30",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Broad_GWAS_supplemental_15061359_A1/idats/200557060038_R10C02/200557060038_R10C02_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Broad_GWAS_supplemental_15061359_A1/idats/200557060038_R10C02/200557060038_R10C02_Red.idat",

diff --git a/...gle_sample/test_inputs/Scientific/200557060038_R10C02_PRISM_7032_PullNoFPFromMercury.json b/...gle_sample/test_inputs/Scientific/200557060038_R10C02_PRISM_7032_PullNoFPFromMercury.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-30",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Broad_GWAS_supplemental_15061359_A1/idats/200557060038_R10C02/200557060038_R10C02_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Broad_GWAS_supplemental_15061359_A1/idats/200557060038_R10C02/200557060038_R10C02_Red.idat",

diff --git a/.../single_sample/test_inputs/Scientific/200557060038_R10C02_PRISM_7032_PushFPToMercury.json b/.../single_sample/test_inputs/Scientific/200557060038_R10C02_PRISM_7032_PushFPToMercury.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-30",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Broad_GWAS_supplemental_15061359_A1/idats/200557060038_R10C02/200557060038_R10C02_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Broad_GWAS_supplemental_15061359_A1/idats/200557060038_R10C02/200557060038_R10C02_Red.idat",

diff --git a/pipelines/broad/arrays/single_sample/test_inputs/Scientific/200557070005_R06C01_NA12878.json b/pipelines/broad/arrays/single_sample/test_inputs/Scientific/200557070005_R06C01_NA12878.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-30",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Broad_GWAS_supplemental_15061359_A1/idats/200557070005_R06C01/200557070005_R06C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Broad_GWAS_supplemental_15061359_A1/idats/200557070005_R06C01/200557070005_R06C01_Red.idat",

diff --git a/...es/broad/arrays/single_sample/test_inputs/Scientific/200557070028_R10C01_PRI_SM_7241.json b/...es/broad/arrays/single_sample/test_inputs/Scientific/200557070028_R10C01_PRI_SM_7241.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-30",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Broad_GWAS_supplemental_15061359_A1/idats/200557070028_R10C01/200557070028_R10C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Broad_GWAS_supplemental_15061359_A1/idats/200557070028_R10C01/200557070028_R10C01_Red.idat",

diff --git a/...es/broad/arrays/single_sample/test_inputs/Scientific/200557070035_R05C02_PRI_SM_8643.json b/...es/broad/arrays/single_sample/test_inputs/Scientific/200557070035_R05C02_PRI_SM_8643.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-30",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Broad_GWAS_supplemental_15061359_A1/idats/200557070035_R05C02/200557070035_R05C02_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Broad_GWAS_supplemental_15061359_A1/idats/200557070035_R05C02/200557070035_R05C02_Red.idat",

diff --git a/...nes/broad/arrays/single_sample/test_inputs/Scientific/200557070035_R06C01_PRISM_7289.json b/...nes/broad/arrays/single_sample/test_inputs/Scientific/200557070035_R06C01_PRISM_7289.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-30",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Broad_GWAS_supplemental_15061359_A1/idats/200557070035_R06C01/200557070035_R06C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Broad_GWAS_supplemental_15061359_A1/idats/200557070035_R06C01/200557070035_R06C01_Red.idat",

diff --git a/...lines/broad/arrays/single_sample/test_inputs/Scientific/200598830050_R01C01_90C04566.json b/...lines/broad/arrays/single_sample/test_inputs/Scientific/200598830050_R01C01_90C04566.json
@@ -17,7 +17,6 @@
   "Arrays.research_project_id": "RP-48",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/PsychChip_v1-1_15073391_A1/idats/200598830050_R01C01/200598830050_R01C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/PsychChip_v1-1_15073391_A1/idats/200598830050_R01C01/200598830050_R01C01_Red.idat",

diff --git a/...ines/broad/arrays/single_sample/test_inputs/Scientific/200598830050_R04C01_07C6_2854.json b/...ines/broad/arrays/single_sample/test_inputs/Scientific/200598830050_R04C01_07C6_2854.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-48",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/PsychChip_v1-1_15073391_A1/idats/200598830050_R04C01/200598830050_R04C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/PsychChip_v1-1_15073391_A1/idats/200598830050_R04C01/200598830050_R04C01_Red.idat",

diff --git a/...lines/broad/arrays/single_sample/test_inputs/Scientific/200598830050_R06C02_01C05949.json b/...lines/broad/arrays/single_sample/test_inputs/Scientific/200598830050_R06C02_01C05949.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-48",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/PsychChip_v1-1_15073391_A1/idats/200598830050_R06C02/200598830050_R06C02_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/PsychChip_v1-1_15073391_A1/idats/200598830050_R06C02/200598830050_R06C02_Red.idat",

diff --git a/...ines/broad/arrays/single_sample/test_inputs/Scientific/200598830050_R07C01_03C_17319.json b/...ines/broad/arrays/single_sample/test_inputs/Scientific/200598830050_R07C01_03C_17319.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-48",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/PsychChip_v1-1_15073391_A1/idats/200598830050_R07C01/200598830050_R07C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/PsychChip_v1-1_15073391_A1/idats/200598830050_R07C01/200598830050_R07C01_Red.idat",

diff --git a/pipelines/broad/arrays/single_sample/test_inputs/Scientific/201004840016_R01C01_NA12878.json b/pipelines/broad/arrays/single_sample/test_inputs/Scientific/201004840016_R01C01_NA12878.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-1244",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Multi-EthnicGlobal_A1/idats/201004840016_R01C01/201004840016_R01C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Multi-EthnicGlobal_A1/idats/201004840016_R01C01/201004840016_R01C01_Red.idat",

diff --git a/...lines/broad/arrays/single_sample/test_inputs/Scientific/201008710016_R01C01_AA484383.json b/...lines/broad/arrays/single_sample/test_inputs/Scientific/201008710016_R01C01_AA484383.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-1244",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Multi-EthnicGlobal_A1/idats/201008710016_R01C01/201008710016_R01C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Multi-EthnicGlobal_A1/idats/201008710016_R01C01/201008710016_R01C01_Red.idat",

diff --git a/.../broad/arrays/single_sample/test_inputs/Scientific/201008710016_R05C01_BMS_000637780.json b/.../broad/arrays/single_sample/test_inputs/Scientific/201008710016_R05C01_BMS_000637780.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-1244",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Multi-EthnicGlobal_A1/idats/201008710016_R05C01/201008710016_R05C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/Multi-EthnicGlobal_A1/idats/201008710016_R05C01/201008710016_R05C01_Red.idat",

diff --git a/...s/broad/arrays/single_sample/test_inputs/Scientific/201096140037_R07C01_20055_118477.json b/...s/broad/arrays/single_sample/test_inputs/Scientific/201096140037_R07C01_20055_118477.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-755",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSAMD-24v1-0_20011747_A1/idats/201096140037_R07C01/201096140037_R07C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSAMD-24v1-0_20011747_A1/idats/201096140037_R07C01/201096140037_R07C01_Red.idat",

diff --git a/...lines/broad/arrays/single_sample/test_inputs/Scientific/201138240147_R05C01_05C49266.json b/...lines/broad/arrays/single_sample/test_inputs/Scientific/201138240147_R05C01_05C49266.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-48",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSAMD-24v1-0_20011747_A1/idats/201138240147_R05C01/201138240147_R05C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSAMD-24v1-0_20011747_A1/idats/201138240147_R05C01/201138240147_R05C01_Red.idat",

diff --git a/...nes/broad/arrays/single_sample/test_inputs/Scientific/201138240147_R08C01_MH_0188385.json b/...nes/broad/arrays/single_sample/test_inputs/Scientific/201138240147_R08C01_MH_0188385.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-48",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSAMD-24v1-0_20011747_A1/idats/201138240147_R08C01/201138240147_R08C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSAMD-24v1-0_20011747_A1/idats/201138240147_R08C01/201138240147_R08C01_Red.idat",

diff --git a/...es/broad/arrays/single_sample/test_inputs/Scientific/201145020059_R07C01_2004_713547.json b/...es/broad/arrays/single_sample/test_inputs/Scientific/201145020059_R07C01_2004_713547.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-755",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSAMD-24v1-0_20011747_A1/idats/201145020059_R07C01/201145020059_R07C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSAMD-24v1-0_20011747_A1/idats/201145020059_R07C01/201145020059_R07C01_Red.idat",

diff --git a/...nes/broad/arrays/single_sample/test_inputs/Scientific/201145020068_R12C01_2004826455.json b/...nes/broad/arrays/single_sample/test_inputs/Scientific/201145020068_R12C01_2004826455.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-755",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSAMD-24v1-0_20011747_A1/idats/201145020068_R12C01/201145020068_R12C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSAMD-24v1-0_20011747_A1/idats/201145020068_R12C01/201145020068_R12C01_Red.idat",

diff --git a/...nes/broad/arrays/single_sample/test_inputs/Scientific/201148280144_R12C01_2005492094.json b/...nes/broad/arrays/single_sample/test_inputs/Scientific/201148280144_R12C01_2005492094.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-755",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSAMD-24v1-0_20011747_A1/idats/201148280144_R12C01/201148280144_R12C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSAMD-24v1-0_20011747_A1/idats/201148280144_R12C01/201148280144_R12C01_Red.idat",

diff --git a/...ines/broad/arrays/single_sample/test_inputs/Scientific/201159110147_R06C01_MH0158716.json b/...ines/broad/arrays/single_sample/test_inputs/Scientific/201159110147_R06C01_MH0158716.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-48",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSA-24v1-0_A1/idats/201159110147_R06C01/201159110147_R06C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSA-24v1-0_A1/idats/201159110147_R06C01/201159110147_R06C01_Red.idat",

diff --git a/...nes/broad/arrays/single_sample/test_inputs/Scientific/201159110147_R09C01_MH_0178994.json b/...nes/broad/arrays/single_sample/test_inputs/Scientific/201159110147_R09C01_MH_0178994.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-48",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSA-24v1-0_A1/idats/201159110147_R09C01/201159110147_R09C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSA-24v1-0_A1/idats/201159110147_R09C01/201159110147_R09C01_Red.idat",

diff --git a/pipelines/broad/arrays/single_sample/test_inputs/Scientific/201179310001_R01C01_NA12878.json b/pipelines/broad/arrays/single_sample/test_inputs/Scientific/201179310001_R01C01_NA12878.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-518",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSA-24v1-0_A1/idats/201179310001_R01C01/201179310001_R01C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSA-24v1-0_A1/idats/201179310001_R01C01/201179310001_R01C01_Red.idat",

diff --git a/pipelines/broad/arrays/single_sample/test_inputs/Scientific/201179310001_R09C01_NA12892.json b/pipelines/broad/arrays/single_sample/test_inputs/Scientific/201179310001_R09C01_NA12892.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-518",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSA-24v1-0_A1/idats/201179310001_R09C01/201179310001_R09C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSA-24v1-0_A1/idats/201179310001_R09C01/201179310001_R09C01_Red.idat",

diff --git a/pipelines/broad/arrays/single_sample/test_inputs/Scientific/201179310001_R12C02_NA12891.json b/pipelines/broad/arrays/single_sample/test_inputs/Scientific/201179310001_R12C02_NA12891.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-518",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSA-24v1-0_A1/idats/201179310001_R12C02/201179310001_R12C02_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSA-24v1-0_A1/idats/201179310001_R12C02/201179310001_R12C02_Red.idat",

diff --git a/pipelines/broad/arrays/single_sample/test_inputs/Scientific/201179320110_R01C01_NA12878.json b/pipelines/broad/arrays/single_sample/test_inputs/Scientific/201179320110_R01C01_NA12878.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-48",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSAMD-24v1-0_20011747_A1/idats/201179320110_R01C01/201179320110_R01C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/GSAMD-24v1-0_20011747_A1/idats/201179320110_R01C01/201179320110_R01C01_Red.idat",

diff --git a/pipelines/broad/arrays/single_sample/test_inputs/Scientific/201490040272_R01C01_NA12878.json b/pipelines/broad/arrays/single_sample/test_inputs/Scientific/201490040272_R01C01_NA12878.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-1169",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumOmniExpressExome-8v1-4_A1/idats/201490040272_R01C01/201490040272_R01C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumOmniExpressExome-8v1-4_A1/idats/201490040272_R01C01/201490040272_R01C01_Red.idat",

diff --git a/pipelines/broad/arrays/single_sample/test_inputs/Scientific/201651070002_R01C01_NA12878.json b/pipelines/broad/arrays/single_sample/test_inputs/Scientific/201651070002_R01C01_NA12878.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-1169",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumOmniExpressExome-8v1-4_A1/idats/201651070002_R01C01/201651070002_R01C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumOmniExpressExome-8v1-4_A1/idats/201651070002_R01C01/201651070002_R01C01_Red.idat",

diff --git a/...ines/broad/arrays/single_sample/test_inputs/Scientific/201651070043_R06C01_SLH_39O71.json b/...ines/broad/arrays/single_sample/test_inputs/Scientific/201651070043_R06C01_SLH_39O71.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-1169",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumOmniExpressExome-8v1-4_A1/idats/201651070043_R06C01/201651070043_R06C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumOmniExpressExome-8v1-4_A1/idats/201651070043_R06C01/201651070043_R06C01_Red.idat",

diff --git a/...ines/broad/arrays/single_sample/test_inputs/Scientific/201651080129_R05C01_S8_N4B3GY.json b/...ines/broad/arrays/single_sample/test_inputs/Scientific/201651080129_R05C01_S8_N4B3GY.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-1169",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumOmniExpressExome-8v1-4_A1/idats/201651080129_R05C01/201651080129_R05C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumOmniExpressExome-8v1-4_A1/idats/201651080129_R05C01/201651080129_R05C01_Red.idat",

diff --git a/...single_sample/test_inputs/Scientific/201651080129_R05C01_S8_N4B3GY_PullFPFromMercury.json b/...single_sample/test_inputs/Scientific/201651080129_R05C01_S8_N4B3GY_PullFPFromMercury.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-1169",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumOmniExpressExome-8v1-4_A1/idats/201651080129_R05C01/201651080129_R05C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumOmniExpressExome-8v1-4_A1/idats/201651080129_R05C01/201651080129_R05C01_Red.idat",

diff --git a/...ample/test_inputs/Scientific/201651080129_R05C01_S8_N4B3GY_PullFPFromMercuryClinical.json b/...ample/test_inputs/Scientific/201651080129_R05C01_S8_N4B3GY_PullFPFromMercuryClinical.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-1169",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumOmniExpressExome-8v1-4_A1/idats/201651080129_R05C01/201651080129_R05C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumOmniExpressExome-8v1-4_A1/idats/201651080129_R05C01/201651080129_R05C01_Red.idat",

diff --git a/...lines/broad/arrays/single_sample/test_inputs/Scientific/201651080129_R06C01_SPT3TC2T.json b/...lines/broad/arrays/single_sample/test_inputs/Scientific/201651080129_R06C01_SPT3TC2T.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-1169",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumOmniExpressExome-8v1-4_A1/idats/201651080129_R06C01/201651080129_R06C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumOmniExpressExome-8v1-4_A1/idats/201651080129_R06C01/201651080129_R06C01_Red.idat",

diff --git a/...lines/broad/arrays/single_sample/test_inputs/Scientific/201651080129_R07C01_S3QG3651.json b/...lines/broad/arrays/single_sample/test_inputs/Scientific/201651080129_R07C01_S3QG3651.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-1169",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumOmniExpressExome-8v1-4_A1/idats/201651080129_R07C01/201651080129_R07C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumOmniExpressExome-8v1-4_A1/idats/201651080129_R07C01/201651080129_R07C01_Red.idat",

diff --git a/pipelines/broad/arrays/single_sample/test_inputs/Scientific/202871110118_R01C01_NA12878.json b/pipelines/broad/arrays/single_sample/test_inputs/Scientific/202871110118_R01C01_NA12878.json
@@ -18,7 +18,6 @@
   "Arrays.research_project_id": "RP-1729",
 
   "Arrays.call_rate_threshold": 0.98,
-  "Arrays.genotype_concordance_threshold": 0.98,
 
   "Arrays.green_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumOmniExpressExome-8v1-6_A1/idats/202871110118_R01C01/202871110118_R01C01_Grn.idat",
   "Arrays.red_idat_cloud_path": "gs://broad-gotc-test-storage/arrays/InfiniumOmniExpressExome-8v1-6_A1/idats/202871110118_R01C01/202871110118_R01C01_Red.idat",