added example data

test/example-data/config.env

@@ -0,0 +1,42 @@
+#!/bin/bash
+
+# To be edited by analysts
+cohort_name="ExampleData"
+analyst_name="Name"
+analyst_email="email@email.com"
+sftp_username="username"
+
+genotype_input_list="geno_input.txt"
+phenotype_input_dir="phen_input"
+phenotype_processed_dir="phen_proc"
+genotype_processed_dir="geno_proc"
+results_dir="results"
+env_family_data="false"
+
+# Provide either hg19 or hg38
+genome_build="hg19"
+
+# Add any study-specific covariate variables that must be included here.
+# We expect this to correspond to a column name in $phenotype_input_dir/pheno_covariates.txt
+# sex and yob are default that should be included
+static_covariates="sex yob batch"
+
+# Choose from one of EUR, EAS, SAS, AFR, AMR, MID
+major_ancestry="EUR"
+
+# Provide a path to a sample inclusion list
+# This should be formatted with just two columns (FID and IID)
+# If it is left blank, all samples will be included
+sample_inclusion_list="phen_input/sample_inclusion.txt"
+
+# Other parameters
+env_minumum_strat_n="100"
+env_n_pcs="10"
+env_sparse_cutoff="0.05"
+env_pca_sd=7
+env_minmaf="0.01"
+env_mininfo="0.8"
+env_hwe="1e-6"
+env_miss="0.05"
+env_imiss="0.05"
+env_threads=1

test/example-data/geno_input.txt

@@ -0,0 +1,23 @@
+/path/to/data_01.bgen /path/to/data.sample
+/path/to/data_02.bgen /path/to/data.sample
+/path/to/data_03.bgen /path/to/data.sample
+/path/to/data_04.bgen /path/to/data.sample
+/path/to/data_05.bgen /path/to/data.sample
+/path/to/data_06.bgen /path/to/data.sample
+/path/to/data_07.bgen /path/to/data.sample
+/path/to/data_08.bgen /path/to/data.sample
+/path/to/data_09.bgen /path/to/data.sample
+/path/to/data_10.bgen /path/to/data.sample
+/path/to/data_11.bgen /path/to/data.sample
+/path/to/data_12.bgen /path/to/data.sample
+/path/to/data_13.bgen /path/to/data.sample
+/path/to/data_14.bgen /path/to/data.sample
+/path/to/data_15.bgen /path/to/data.sample
+/path/to/data_16.bgen /path/to/data.sample
+/path/to/data_17.bgen /path/to/data.sample
+/path/to/data_18.bgen /path/to/data.sample
+/path/to/data_19.bgen /path/to/data.sample
+/path/to/data_20.bgen /path/to/data.sample
+/path/to/data_21.bgen /path/to/data.sample
+/path/to/data_22.bgen /path/to/data.sample
+/path/to/data_23.bgen /path/to/data.sample

test/example-data/phen_input/adiponectin.txt

@@ -0,0 +1,101 @@
+FID	IID	value	age
+5258	5258	20.35	25.25
+2571	2571	60.36	73.08
+2600	2600	4.98	57.83
+8441	8441	69.29	60.08
+2973	2973	64.38	20.5
+4227	4227	74.88	50.83
+5180	5180	57.45	34.08
+7201	7201	80.98	70.5
+7941	7941	96.29	50.67
+6903	6903	84	79.92
+7973	7973	11.76	69.08
+8290	8290	75.9	41.92
+1110	1110	32.78	70.92
+3555	3555	89.45	33.5
+7514	7514	28.63	78.25
+8588	8588	9.99	21.83
+9697	9697	33.78	33.17
+5672	5672	87.2	75.58
+1697	1697	21.16	56
+1824	1824	54.47	58.83
+4544	4544	24.24	50.25
+9559	9559	33.04	40.92
+1458	1458	97.65	39.75
+1328	1328	43.48	39.08
+9473	9473	97.64	20.08
+4381	4381	98.26	38.58
+4957	4957	26.21	26.75
+5768	5768	17.74	62.92
+9295	9295	64.39	40.42
+3236	3236	8.66	66.33
+6958	6958	1.54	74.83
+9594	9594	4.11	28.17
+8956	8956	44.82	61.42
+7576	7576	74.53	51.67
+7980	7980	98.84	31.5
+5728	5728	53.86	59.92
+9675	9675	25.11	31.92
+6590	6590	67.34	24.75
+9794	9794	23.94	63.33
+2297	2297	29.44	63.92
+2008	2008	57.36	38.42
+7342	7342	43.4	77.25
+7162	7162	56.56	53.42
+9931	9931	65.65	22.75
+4331	4331	87.64	59.83
+3044	3044	42.6	20.92
+8002	8002	93.17	71.75
+4772	4772	54.03	26.42
+5939	5939	88.2	45
+3697	3697	56.67	63.83
+2443	2443	68.94	52.58
+7520	7520	93.22	46.83
+6766	6766	23.42	72.75
+2884	2884	40.9	46.5
+1164	1164	27.93	75.92
+3613	3613	83.93	27.25
+7889	7889	21.27	23.67
+9721	9721	39.44	63.58
+5851	5851	67.54	26.25
+7915	7915	17.37	52.67
+6345	6345	78.98	26.67
+3878	3878	38.07	47.17
+1880	1880	60.96	74.5
+6628	6628	37.9	49.33
+7849	7849	12.62	79.58
+1758	1758	60.99	47.25
+7625	7625	73.85	38.08
+1221	1221	99.4	23.33
+9939	9939	57.51	28
+2065	2065	26.09	54.08
+4925	4925	96.48	33.08
+8198	8198	30.93	30.92
+8325	8325	10.5	20.33
+4195	4195	77.35	21.42
+8883	8883	75.44	78.58
+2636	2636	23.57	29.5
+3516	3516	32.11	52.5
+6893	6893	67.2	46.42
+9385	9385	59.07	57.5
+6755	6755	33.59	78.5
+6989	6989	43.44	24.92
+3556	3556	94.76	39.42
+7671	7671	25.28	66.75
+4176	4176	12.28	65.83
+7774	7774	98.65	61.92
+7387	7387	95.53	57.75
+9235	9235	30.9	54.75
+6559	6559	47.52	58.67
+8756	8756	71.97	30.17
+9240	9240	38.55	69.67
+4763	4763	34.2	58.42
+8593	8593	35.1	24.5
+7081	7081	46.07	60.25
+6336	6336	41.11	64.5
+5991	5991	73.84	79.5
+2538	2538	21.26	48.25
+5158	5158	25.64	56.17
+3338	3338	50.04	28.42
+4062	4062	3.89	70.33
+9635	9635	47.93	46.17

test/example-data/phen_input/bmi.txt

@@ -0,0 +1,101 @@
+FID	IID	value	age
+5258	5258	39.7	25.25
+2571	2571	4.75	73.08
+2600	2600	53.47	57.83
+8441	8441	3.01	60.08
+2973	2973	34.94	20.5
+4227	4227	23.23	50.83
+5180	5180	31.82	34.08
+7201	7201	10.65	70.5
+7941	7941	27.41	50.67
+6903	6903	38.99	79.92
+7973	7973	21.12	69.08
+8290	8290	13.43	41.92
+1110	1110	20.41	70.92
+3555	3555	53.69	33.5
+7514	7514	41.37	78.25
+8588	8588	23.21	21.83
+9697	9697	3.49	33.17
+5672	5672	8.33	75.58
+1697	1697	24.12	56
+1824	1824	52.46	58.83
+4544	4544	12.22	50.25
+9559	9559	6.99	40.92
+1458	1458	51.23	39.75
+1328	1328	15.51	39.08
+9473	9473	1.45	20.08
+4381	4381	4.03	38.58
+4957	4957	23.74	26.75
+5768	5768	58.49	62.92
+9295	9295	10.06	40.42
+3236	3236	27.01	66.33
+6958	6958	1.59	74.83
+9594	9594	19.33	28.17
+8956	8956	46.32	61.42
+7576	7576	25.11	51.67
+7980	7980	37.28	31.5
+5728	5728	4.03	59.92
+9675	9675	44.77	31.92
+6590	6590	29.71	24.75
+9794	9794	43.93	63.33
+2297	2297	10.76	63.92
+2008	2008	16.18	38.42
+7342	7342	39.48	77.25
+7162	7162	42.9	53.42
+9931	9931	11.1	22.75
+4331	4331	29.7	59.83
+3044	3044	19.28	20.92
+8002	8002	19.23	71.75
+4772	4772	9.96	26.42
+5939	5939	57.4	45
+3697	3697	21.01	63.83
+2443	2443	59.49	52.58
+7520	7520	17.29	46.83
+6766	6766	27.32	72.75
+2884	2884	2.1	46.5
+1164	1164	2.82	75.92
+3613	3613	20.43	27.25
+7889	7889	45.27	23.67
+9721	9721	55.58	63.58
+5851	5851	23.59	26.25
+7915	7915	48.7	52.67
+6345	6345	7.38	26.67
+3878	3878	28.14	47.17
+1880	1880	53.62	74.5
+6628	6628	9.03	49.33
+7849	7849	7.14	79.58
+1758	1758	17.25	47.25
+7625	7625	55.45	38.08
+1221	1221	33.38	23.33
+9939	9939	44.06	28
+2065	2065	42.39	54.08
+4925	4925	3.48	33.08
+8198	8198	19.28	30.92
+8325	8325	59.13	20.33
+4195	4195	25.9	21.42
+8883	8883	14.01	78.58
+2636	2636	5.68	29.5
+3516	3516	21.39	52.5
+6893	6893	45.61	46.42
+9385	9385	6.07	57.5
+6755	6755	54.29	78.5
+6989	6989	38.71	24.92
+3556	3556	1.42	39.42
+7671	7671	58.29	66.75
+4176	4176	44.94	65.83
+7774	7774	26.1	61.92
+7387	7387	16.51	57.75
+9235	9235	20.23	54.75
+6559	6559	59.62	58.67
+8756	8756	54.82	30.17
+9240	9240	46.53	69.67
+4763	4763	52.17	58.42
+8593	8593	23.6	24.5
+7081	7081	26.21	60.25
+6336	6336	38.22	64.5
+5991	5991	38.13	79.5
+2538	2538	29.11	48.25
+5158	5158	41.44	56.17
+3338	3338	4.13	28.42
+4062	4062	26.42	70.33
+9635	9635	10.52	46.17

test/example-data/phen_input/calcium.txt

@@ -0,0 +1,101 @@
+FID	IID	value	age
+5258	5258	4.57	25.25
+2571	2571	5.73	73.08
+2600	2600	5.79	57.83
+8441	8441	3.6	60.08
+2973	2973	8.28	20.5
+4227	4227	9.76	50.83
+5180	5180	1.59	34.08
+7201	7201	0.96	70.5
+7941	7941	0.81	50.67
+6903	6903	2.99	79.92
+7973	7973	2.09	69.08
+8290	8290	9.67	41.92
+1110	1110	7.86	70.92
+3555	3555	7.3	33.5
+7514	7514	6.68	78.25
+8588	8588	9.6	21.83
+9697	9697	3.02	33.17
+5672	5672	6.87	75.58
+1697	1697	5.64	56
+1824	1824	0.77	58.83
+4544	4544	0.33	50.25
+9559	9559	9.91	40.92
+1458	1458	9.67	39.75
+1328	1328	1.04	39.08
+9473	9473	5.97	20.08
+4381	4381	5.42	38.58
+4957	4957	8.03	26.75
+5768	5768	4.03	62.92
+9295	9295	7.98	40.42
+3236	3236	4.93	66.33
+6958	6958	9.64	74.83
+9594	9594	9.26	28.17
+8956	8956	0.33	61.42
+7576	7576	2.64	51.67
+7980	7980	7.51	31.5
+5728	5728	9.13	59.92
+9675	9675	2.66	31.92
+6590	6590	4.54	24.75
+9794	9794	3.79	63.33
+2297	2297	7.52	63.92
+2008	2008	2.81	38.42
+7342	7342	5.31	77.25
+7162	7162	4.79	53.42
+9931	9931	7.54	22.75
+4331	4331	7.76	59.83
+3044	3044	2.58	20.92
+8002	8002	3.62	71.75
+4772	4772	6.4	26.42
+5939	5939	6.97	45
+3697	3697	6.16	63.83
+2443	2443	3.56	52.58
+7520	7520	4.47	46.83
+6766	6766	9.97	72.75
+2884	2884	7.35	46.5
+1164	1164	6.26	75.92
+3613	3613	7.38	27.25
+7889	7889	0.01	23.67
+9721	9721	0.42	63.58
+5851	5851	6.27	26.25
+7915	7915	5.05	52.67
+6345	6345	1.01	26.67
+3878	3878	8.96	47.17
+1880	1880	3.82	74.5
+6628	6628	8.95	49.33
+7849	7849	6.42	79.58
+1758	1758	1.16	47.25
+7625	7625	3.42	38.08
+1221	1221	9.58	23.33
+9939	9939	0.68	28
+2065	2065	9.62	54.08
+4925	4925	1.37	33.08
+8198	8198	9.22	30.92
+8325	8325	4.4	20.33
+4195	4195	2.94	21.42
+8883	8883	5.66	78.58
+2636	2636	1.97	29.5
+3516	3516	4.35	52.5
+6893	6893	7.06	46.42
+9385	9385	8.89	57.5
+6755	6755	3.57	78.5
+6989	6989	3.16	24.92
+3556	3556	1.25	39.42
+7671	7671	4.63	66.75
+4176	4176	0.93	65.83
+7774	7774	2.14	61.92
+7387	7387	9.45	57.75
+9235	9235	0.52	54.75
+6559	6559	5.4	58.67
+8756	8756	5.39	30.17
+9240	9240	2.67	69.67
+4763	4763	9.56	58.42
+8593	8593	8.22	24.5
+7081	7081	3.03	60.25
+6336	6336	5.58	64.5
+5991	5991	4.82	79.5
+2538	2538	8.84	48.25
+5158	5158	4.77	56.17
+3338	3338	1.15	28.42
+4062	4062	7	70.33
+9635	9635	4.83	46.17