## htsjdk.samtools.metrics.StringHeader
# CollectHsMetrics BAIT_INTERVALS=[/gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/agilent/SureSelect_Clinical_Research_Exome_V2_S30409818_Regions_hg38.interval_list] BAIT_SET_NAME=SureSelect_Clinical_Research_Exome_V2_crossmap_hg38 TARGET_INTERVALS=[/gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/agilent/SureSelect_Clinical_Research_Exome_V2_S30409818_Padded_hg38.interval_list] INPUT=/gpfs/share/cmoco_sys_dev/nfs/storage/cromwell/cromwell-executions/PairedEndSingleSampleWorkflow/1a92739a-b912-4025-8cfa-af33c8b5b897/call-CollectPerTargetHsMetrics_Exome/inputs/gpfs/share/cmoco_sys_dev/nfs/storage/cromwell/cromwell-executions/PairedEndSingleSampleWorkflow/1a92739a-b912-4025-8cfa-af33c8b5b897/call-ApplyBQSR/execution/NA12878.lValExome0030.bam OUTPUT=NA12878.lValExome0030.hs_metrics.exome.all_reads PER_TARGET_COVERAGE=NA12878.lValExome0030.hs_metrics.exome.per_target_coverage REFERENCE_SEQUENCE=/gpfs/share/cmoco_sys_dev/nfs/storage/germline/resources/gatk_bundle/Homo_sapiens_assembly38.fasta    METRIC_ACCUMULATION_LEVEL=[ALL_READS] NEAR_DISTANCE=250 MINIMUM_MAPPING_QUALITY=20 MINIMUM_BASE_QUALITY=20 CLIP_OVERLAPPING_READS=true COVERAGE_CAP=200 SAMPLE_SIZE=10000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=5 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Sat Mar 03 13:23:33 UTC 2018

## METRICS CLASS	picard.analysis.directed.HsMetrics
BAIT_SET	GENOME_SIZE	BAIT_TERRITORY	TARGET_TERRITORY	BAIT_DESIGN_EFFICIENCY	TOTAL_READS	PF_READS	PF_UNIQUE_READS	PCT_PF_READS	PCT_PF_UQ_READS	PF_UQ_READS_ALIGNED	PCT_PF_UQ_READS_ALIGNED	PF_BASES_ALIGNED	PF_UQ_BASES_ALIGNED	ON_BAIT_BASES	NEAR_BAIT_BASES	OFF_BAIT_BASES	ON_TARGET_BASES	PCT_SELECTED_BASES	PCT_OFF_BAIT	ON_BAIT_VS_SELECTED	MEAN_BAIT_COVERAGE	MEAN_TARGET_COVERAGE	MEDIAN_TARGET_COVERAGE	MAX_TARGET_COVERAGE	PCT_USABLE_BASES_ON_BAIT	PCT_USABLE_BASES_ON_TARGET	FOLD_ENRICHMENT	ZERO_CVG_TARGETS_PCT	PCT_EXC_DUPE	PCT_EXC_MAPQ	PCT_EXC_BASEQ	PCT_EXC_OVERLAP	PCT_EXC_OFF_TARGET	FOLD_80_BASE_PENALTY	PCT_TARGET_BASES_1X	PCT_TARGET_BASES_2X	PCT_TARGET_BASES_10X	PCT_TARGET_BASES_20X	PCT_TARGET_BASES_30X	PCT_TARGET_BASES_40X	PCT_TARGET_BASES_50X	PCT_TARGET_BASES_100X	HS_LIBRARY_SIZE	HS_PENALTY_10X	HS_PENALTY_20X	HS_PENALTY_30X	HS_PENALTY_40X	HS_PENALTY_50X	HS_PENALTY_100X	AT_DROPOUT	GC_DROPOUT	HET_SNP_SENSITIVITY	HET_SNP_Q	SAMPLE	LIBRARY	READ_GROUP
SureSelect_Clinical_Research_Exome_V2_crossmap_hg38	3217346917	67107820	111990327	1.668812	265149104	265149104	238011783	1	0.897653	225067577	0.945615	39656259319	35702817708	22306324654	7953256310	9396678355	19160838896	0.763047	0.236953	0.737166	332.39531	171.093695	139	6910	0.561467	0.482293	26.967522	0.015919	0.099693	0.002361	0.016998	0.17413	0.719236	2.592329	0.982806	0.981287	0.973994	0.961379	0.939814	0.908095	0.869087	0.656378	439706133	4.910855	4.988941	5.078596	5.162466	5.261375	5.802773	8.445949	0.634126	0.979332	17			

## HISTOGRAM	java.lang.Integer
coverage_or_base_quality	high_quality_coverage_count	unfiltered_baseq_count
0	1925528	0
1	170193	0
2	118984	0
3	103465	92
4	96078	4600
5	95731	913690
6	96706	22050932
7	99209	0
8	101658	0
9	104874	0
10	109339	472335751
11	115057	0
12	121734	0
13	128071	0
14	135285	0
15	144133	0
16	150001	0
17	159705	0
18	169535	0
19	179925	0
20	189427	587752401
21	199794	0
22	212733	0
23	223850	0
24	234323	0
25	246151	0
26	259264	0
27	271183	0
28	283041	0
29	295293	0
30	306509	13967683706
31	318745	0
32	328791	0
33	339602	0
34	351220	0
35	361213	0
36	371914	0
37	382500	0
38	391476	0
39	400284	0
40	409244	0
41	415538	0
42	422524	0
43	429438	0
44	436799	0
45	441694	0
46	447325	0
47	451466	0
48	455205	0
49	459233	0
50	462531	0
51	466077	0
52	470049	0
53	470843	0
54	472356	0
55	474125	0
56	476250	0
57	476786	0
58	478597	0
59	479026	0
60	481126	0
61	480905	0
62	482042	0
63	482972	0
64	483403	0
65	483185	0
66	483884	0
67	483211	0
68	482540	0
69	482317	0
70	483949	0
71	483474	0
72	483183	0
73	482095	0
74	480991	0
75	482118	0
76	480910	0
77	481321	0
78	480022	0
79	480457	0
80	478981	0
81	478690	0
82	478079	0
83	476418	0
84	477837	0
85	477298	0
86	477357	0
87	476018	0
88	473937	0
89	474104	0
90	472043	0
91	472297	0
92	471041	0
93	469615	0
94	468386	0
95	467487	0
96	466602	0
97	465561	0
98	464490	0
99	464342	0
100	463146	0
101	462931	0
102	462511	0
103	459236	0
104	458695	0
105	456821	0
106	456993	0
107	455699	0
108	454435	0
109	453917	0
110	452600	0
111	449968	0
112	451680	0
113	448999	0
114	448072	0
115	447837	0
116	444701	0
117	442984	0
118	442889	0
119	440093	0
120	438806	0
121	437115	0
122	435214	0
123	433113	0
124	432247	0
125	431045	0
126	429646	0
127	429197	0
128	426617	0
129	426585	0
130	424437	0
131	422632	0
132	420065	0
133	417773	0
134	415735	0
135	414725	0
136	413012	0
137	409929	0
138	409551	0
139	407465	0
140	405755	0
141	405048	0
142	401212	0
143	400208	0
144	398303	0
145	396440	0
146	394967	0
147	391216	0
148	388856	0
149	388343	0
150	386324	0
151	382683	0
152	380797	0
153	379273	0
154	376597	0
155	374915	0
156	373120	0
157	371389	0
158	369356	0
159	366884	0
160	364257	0
161	362887	0
162	360875	0
163	358998	0
164	357240	0
165	354731	0
166	353870	0
167	350350	0
168	348886	0
169	347904	0
170	345008	0
171	342709	0
172	340061	0
173	338448	0
174	336320	0
175	333513	0
176	332319	0
177	330039	0
178	327871	0
179	326032	0
180	323314	0
181	321617	0
182	320678	0
183	317357	0
184	316234	0
185	313946	0
186	311722	0
187	309225	0
188	308732	0
189	305720	0
190	304414	0
191	303691	0
192	300945	0
193	299753	0
194	297485	0
195	294699	0
196	292568	0
197	291136	0
198	288498	0
199	287755	0
200	35225400	0

