## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/star/hg38-NP_Day10_supernatant_TA_A71_S7.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/hg38-NP_Day10_supernatant_TA_A71_S7.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/hg38-NP_Day10_supernatant_TA_A71_S7.samtools-coordinate.metrics.txt    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 SORTING_COLLECTION_SIZE_RATIO=0.25 TAG_DUPLICATE_SET_MEMBERS=false REMOVE_SEQUENCING_DUPLICATES=false TAGGING_POLICY=DontTag CLEAR_DT=true DUPLEX_UMI=false ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX=<optimized capture of last three ':' separated fields as numeric values> OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 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: Mon Aug 30 14:11:43 CEST 2021

## METRICS CLASS	picard.sam.DuplicationMetrics
LIBRARY	UNPAIRED_READS_EXAMINED	READ_PAIRS_EXAMINED	SECONDARY_OR_SUPPLEMENTARY_RDS	UNMAPPED_READS	UNPAIRED_READ_DUPLICATES	READ_PAIR_DUPLICATES	READ_PAIR_OPTICAL_DUPLICATES	PERCENT_DUPLICATION	ESTIMATED_LIBRARY_SIZE
Unknown Library	192	14056657	0	0	91	3333225	3854	0.237129	24760355

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000204	8328809	0	8330966
2.0	1.567142	1909126	3847	1908147
3.0	1.888496	369907	2	369052
4.0	2.070647	70245	1	70018
5.0	2.173894	16972	0	16895
6.0	2.232417	6637	0	6627
7.0	2.265589	3703	0	3699
8.0	2.284392	2436	0	2435
9.0	2.295049	1871	0	1870
10.0	2.30109	1375	0	1378
11.0	2.304515	1119	0	1117
12.0	2.306456	940	0	939
13.0	2.307556	703	0	701
14.0	2.308179	640	0	639
15.0	2.308533	533	0	534
16.0	2.308733	469	0	469
17.0	2.308847	417	0	419
18.0	2.308911	365	0	363
19.0	2.308948	327	0	328
20.0	2.308968	278	0	276
21.0	2.30898	248	0	249
22.0	2.308987	246	0	246
23.0	2.30899	243	0	242
24.0	2.308993	185	0	186
25.0	2.308994	200	0	199
26.0	2.308994	161	0	162
27.0	2.308995	159	0	159
28.0	2.308995	120	0	119
29.0	2.308995	122	0	122
30.0	2.308995	105	0	107
31.0	2.308995	104	0	102
32.0	2.308995	91	0	92
33.0	2.308995	100	0	99
34.0	2.308995	102	0	103
35.0	2.308995	79	0	78
36.0	2.308995	69	0	69
37.0	2.308995	76	0	76
38.0	2.308995	73	0	73
39.0	2.308995	81	0	81
40.0	2.308995	73	0	75
41.0	2.308995	48	0	46
42.0	2.308995	58	0	58
43.0	2.308995	43	0	43
44.0	2.308995	50	0	50
45.0	2.308995	43	0	43
46.0	2.308995	48	0	48
47.0	2.308995	35	0	35
48.0	2.308995	54	0	54
49.0	2.308995	52	0	52
50.0	2.308995	28	0	28
51.0	2.308995	37	0	38
52.0	2.308995	35	0	34
53.0	2.308995	42	0	43
54.0	2.308995	40	0	39
55.0	2.308995	31	0	31
56.0	2.308995	27	0	27
57.0	2.308995	22	0	22
58.0	2.308995	21	0	22
59.0	2.308995	27	0	26
60.0	2.308995	29	0	30
61.0	2.308995	18	0	17
62.0	2.308995	21	0	21
63.0	2.308995	21	0	21
64.0	2.308995	30	0	31
65.0	2.308995	17	0	18
66.0	2.308995	20	0	18
67.0	2.308995	23	0	23
68.0	2.308995	17	0	17
69.0	2.308995	20	0	20
70.0	2.308995	21	0	21
71.0	2.308995	20	0	20
72.0	2.308995	18	0	18
73.0	2.308995	8	0	8
74.0	2.308995	22	0	22
75.0	2.308995	20	0	20
76.0	2.308995	15	0	15
77.0	2.308995	12	0	12
78.0	2.308995	17	0	17
79.0	2.308995	20	0	20
80.0	2.308995	13	0	14
81.0	2.308995	16	0	15
82.0	2.308995	11	0	11
83.0	2.308995	8	0	8
84.0	2.308995	14	0	14
85.0	2.308995	7	0	7
86.0	2.308995	8	0	8
87.0	2.308995	6	0	6
88.0	2.308995	4	0	4
89.0	2.308995	12	0	12
90.0	2.308995	10	0	10
91.0	2.308995	11	0	11
92.0	2.308995	10	0	11
93.0	2.308995	6	0	5
94.0	2.308995	6	0	6
95.0	2.308995	6	0	6
96.0	2.308995	8	0	8
97.0	2.308995	4	0	4
98.0	2.308995	11	0	11
99.0	2.308995	10	0	10
100.0	2.308995	5	0	5
101.0	0	10	0	10
102.0	0	6	0	6
103.0	0	7	0	7
104.0	0	6	0	6
105.0	0	7	0	8
106.0	0	6	0	5
107.0	0	6	0	6
108.0	0	5	0	5
109.0	0	12	0	12
110.0	0	5	0	5
111.0	0	8	0	9
112.0	0	7	0	6
113.0	0	9	0	10
114.0	0	9	0	8
115.0	0	7	0	7
116.0	0	4	0	4
117.0	0	3	0	3
118.0	0	6	0	6
119.0	0	7	0	7
120.0	0	3	0	3
121.0	0	3	0	3
122.0	0	7	0	7
123.0	0	3	0	3
124.0	0	1	0	1
125.0	0	3	0	3
126.0	0	3	0	3
127.0	0	4	0	4
128.0	0	1	0	1
129.0	0	7	0	7
130.0	0	3	0	3
131.0	0	2	0	2
132.0	0	6	0	6
133.0	0	5	0	5
134.0	0	6	0	6
135.0	0	1	0	1
136.0	0	6	0	6
137.0	0	4	0	4
138.0	0	1	0	1
139.0	0	1	0	1
140.0	0	4	0	4
141.0	0	8	0	8
142.0	0	3	0	3
143.0	0	2	0	2
144.0	0	2	0	2
145.0	0	3	0	3
146.0	0	1	0	1
147.0	0	2	0	2
148.0	0	2	0	2
149.0	0	1	0	1
150.0	0	3	0	3
152.0	0	1	0	1
153.0	0	3	0	3
154.0	0	2	0	2
155.0	0	1	0	1
156.0	0	3	0	3
157.0	0	1	0	1
158.0	0	3	0	3
159.0	0	1	0	1
160.0	0	5	0	5
161.0	0	2	0	2
163.0	0	1	0	1
164.0	0	2	0	2
165.0	0	1	0	1
167.0	0	3	0	3
168.0	0	2	0	2
169.0	0	1	0	1
171.0	0	2	0	2
172.0	0	3	0	3
173.0	0	1	0	2
174.0	0	1	0	0
175.0	0	1	0	1
176.0	0	5	0	6
177.0	0	3	0	2
179.0	0	1	0	1
180.0	0	1	0	1
181.0	0	1	0	1
182.0	0	2	0	2
183.0	0	1	0	1
184.0	0	3	0	3
185.0	0	3	0	3
186.0	0	2	0	2
190.0	0	3	0	3
191.0	0	1	0	1
192.0	0	2	0	2
193.0	0	1	0	1
194.0	0	3	0	3
196.0	0	1	0	1
197.0	0	1	0	1
198.0	0	1	0	1
199.0	0	2	0	2
200.0	0	1	0	1
203.0	0	3	0	3
205.0	0	1	0	2
206.0	0	1	0	0
207.0	0	1	0	1
208.0	0	3	0	3
209.0	0	1	0	1
210.0	0	2	0	2
211.0	0	1	0	1
212.0	0	3	0	3
213.0	0	2	0	2
214.0	0	1	0	1
216.0	0	2	0	2
219.0	0	1	0	1
220.0	0	3	0	3
221.0	0	2	0	2
222.0	0	3	0	3
224.0	0	2	0	2
225.0	0	2	0	2
226.0	0	2	0	2
228.0	0	2	0	2
230.0	0	1	0	1
232.0	0	1	0	1
233.0	0	2	0	2
234.0	0	0	0	1
235.0	0	1	0	0
236.0	0	3	0	3
238.0	0	1	0	1
239.0	0	1	0	1
241.0	0	1	0	1
242.0	0	1	0	1
248.0	0	3	0	3
253.0	0	3	0	4
254.0	0	1	0	0
256.0	0	1	0	1
257.0	0	1	0	1
258.0	0	1	0	1
259.0	0	0	0	1
260.0	0	1	0	0
261.0	0	2	0	2
263.0	0	1	0	1
271.0	0	1	0	1
274.0	0	1	0	1
277.0	0	1	0	1
278.0	0	1	0	1
280.0	0	1	0	1
288.0	0	1	0	2
290.0	0	1	0	1
291.0	0	1	0	0
293.0	0	1	0	1
295.0	0	1	0	1
301.0	0	1	0	1
304.0	0	1	0	1
305.0	0	1	0	1
306.0	0	1	0	1
307.0	0	1	0	1
309.0	0	2	0	2
310.0	0	1	0	1
314.0	0	1	0	1
315.0	0	1	0	1
318.0	0	0	0	1
319.0	0	1	0	0
327.0	0	1	0	1
340.0	0	0	0	1
341.0	0	2	0	1
361.0	0	1	0	1
363.0	0	1	0	1
378.0	0	1	0	1
387.0	0	1	0	1
392.0	0	1	0	1
434.0	0	1	0	1
460.0	0	1	0	1
467.0	0	1	0	1
480.0	0	1	0	1
489.0	0	1	0	1
502.0	0	1	0	1
506.0	0	2	0	2
541.0	0	1	0	1
545.0	0	1	0	1
566.0	0	1	0	1
601.0	0	1	0	1
650.0	0	0	0	1
651.0	0	1	0	0
727.0	0	1	0	1
738.0	0	1	0	1
739.0	0	1	0	1
742.0	0	1	0	1
779.0	0	0	0	1
780.0	0	1	0	0
835.0	0	1	0	1
881.0	0	1	0	1
884.0	0	0	0	1
885.0	0	1	0	0
886.0	0	0	0	1
887.0	0	1	0	0
942.0	0	1	0	1