## htsjdk.samtools.metrics.StringHeader
# CollectWgsMetrics INPUT=/mnt/nfsscratch/npacalin/data/032818_cfdna/cfdnapipeline-output/mapped/NaomicfDNA2_S2_R1.bam OUTPUT=/mnt/nfsscratch/npacalin/data/032818_cfdna/cfdnapipeline-output/alignment-metrics/NaomicfDNA2_S2_R1.wgs_metrics.txt MINIMUM_MAPPING_QUALITY=5 MINIMUM_BASE_QUALITY=10 INCLUDE_BQ_HISTOGRAM=true REFERENCE_SEQUENCE=/mnt/data/pipeline_genome_data/hg19/male.hg19.fa    COVERAGE_CAP=250 LOCUS_ACCUMULATION_CAP=100000 STOP_AFTER=-1 COUNT_UNPAIRED=false SAMPLE_SIZE=10000 USE_FAST_ALGORITHM=false READ_LENGTH=150 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: Tue Apr 03 00:38:05 PDT 2018

## METRICS CLASS	picard.analysis.CollectWgsMetrics$WgsMetrics
GENOME_TERRITORY	MEAN_COVERAGE	SD_COVERAGE	MEDIAN_COVERAGE	MAD_COVERAGE	PCT_EXC_MAPQ	PCT_EXC_DUPE	PCT_EXC_UNPAIRED	PCT_EXC_BASEQ	PCT_EXC_OVERLAP	PCT_EXC_CAPPED	PCT_EXC_TOTAL	PCT_1X	PCT_5X	PCT_10X	PCT_15X	PCT_20X	PCT_25X	PCT_30X	PCT_40X	PCT_50X	PCT_60X	PCT_70X	PCT_80X	PCT_90X	PCT_100X	HET_SNP_SENSITIVITY	HET_SNP_Q
2858674665	2.502973	3.121323	2	1	0.07313	0	0.005564	0.000018	0.009081	0.027927	0.115719	0.844131	0.144866	0.008252	0.001134	0.000536	0.000392	0.000318	0.00024	0.000197	0.000168	0.000147	0.000133	0.000121	0.000111	0.426167	2

## HISTOGRAM	java.lang.Integer
coverage	high_quality_coverage_count	unfiltered_baseq_count
0	445579329	0
1	614778019	0
2	608913727	0
3	467833737	0
4	307444076	0
5	183378260	0
6	103178250	0
7	56484605	0
8	30702067	0
9	16792483	0
10	9316539	0
11	5230690	0
12	2997152	0
13	1753727	0
14	1051642	336981024
15	653460	0
16	420047	0
17	285334	0
18	200025	0
19	148159	0
20	115552	0
21	93612	60280241
22	78914	0
23	67447	0
24	58613	0
25	51754	0
26	46468	0
27	41562	145836648
28	37072	0
29	33307	0
30	31055	0
31	28184	0
32	25653	568424302
33	23731	0
34	22126	0
35	20431	0
36	19751	6108052279
37	18297	0
38	17486	0
39	16331	0
40	15493	0
41	14191	0
42	13921	0
43	13117	0
44	12159	0
45	11942	0
46	11274	0
47	10909	0
48	10618	0
49	9615	0
50	9763	0
51	9501	0
52	9060	0
53	8632	0
54	8364	0
55	8018	0
56	7779	0
57	7465	0
58	7336	0
59	6998	0
60	6813	0
61	6506	0
62	6351	0
63	6069	0
64	5744	0
65	5823	0
66	5492	0
67	5394	0
68	5141	0
69	4884	0
70	4833	0
71	4610	0
72	4534	0
73	4465	0
74	4337	0
75	4192	0
76	3980	0
77	3915	0
78	3879	0
79	4000	0
80	3624	0
81	3547	0
82	3460	0
83	3296	0
84	3292	0
85	3420	0
86	3310	0
87	3247	0
88	3167	0
89	3001	0
90	3025	0
91	2936	0
92	2901	0
93	2902	0
94	2701	0
95	2802	0
96	2659	0
97	2664	0
98	2508	0
99	2431	0
100	2375	0
101	2384	0
102	2293	0
103	2145	0
104	2179	0
105	2106	0
106	2068	0
107	2131	0
108	1985	0
109	1972	0
110	2050	0
111	1964	0
112	1891	0
113	1766	0
114	1795	0
115	1860	0
116	1722	0
117	1754	0
118	1727	0
119	1784	0
120	1664	0
121	1581	0
122	1558	0
123	1541	0
124	1567	0
125	1480	0
126	1417	0
127	1422	0
128	1539	0
129	1499	0
130	1455	0
131	1438	0
132	1368	0
133	1419	0
134	1343	0
135	1325	0
136	1171	0
137	1361	0
138	1240	0
139	1344	0
140	1348	0
141	1279	0
142	1274	0
143	1201	0
144	1182	0
145	1135	0
146	1146	0
147	1105	0
148	1120	0
149	1162	0
150	1102	0
151	1139	0
152	1162	0
153	995	0
154	995	0
155	1091	0
156	1019	0
157	1027	0
158	1008	0
159	992	0
160	975	0
161	1002	0
162	978	0
163	1006	0
164	987	0
165	922	0
166	906	0
167	932	0
168	895	0
169	903	0
170	977	0
171	932	0
172	997	0
173	990	0
174	853	0
175	817	0
176	957	0
177	905	0
178	855	0
179	879	0
180	829	0
181	839	0
182	760	0
183	833	0
184	830	0
185	812	0
186	827	0
187	854	0
188	841	0
189	787	0
190	826	0
191	797	0
192	767	0
193	789	0
194	734	0
195	726	0
196	794	0
197	782	0
198	806	0
199	767	0
200	743	0
201	702	0
202	732	0
203	708	0
204	768	0
205	706	0
206	767	0
207	693	0
208	685	0
209	700	0
210	732	0
211	677	0
212	677	0
213	658	0
214	705	0
215	653	0
216	632	0
217	676	0
218	623	0
219	628	0
220	631	0
221	654	0
222	640	0
223	620	0
224	618	0
225	669	0
226	596	0
227	599	0
228	621	0
229	571	0
230	577	0
231	544	0
232	581	0
233	572	0
234	555	0
235	503	0
236	495	0
237	528	0
238	500	0
239	494	0
240	501	0
241	503	0
242	472	0
243	546	0
244	579	0
245	517	0
246	569	0
247	511	0
248	532	0
249	513	0
250	161472	0