## 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_Day1_adherentcells_DMSO_A70_S14.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/hg38-NP_Day1_adherentcells_DMSO_A70_S14.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/hg38-NP_Day1_adherentcells_DMSO_A70_S14.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 14:05:10 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	225	17260223	0	0	107	1565702	5131	0.090714	89551145

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.00027	14612531	0	14616826
2.0	1.825187	924054	5125	920416
3.0	2.505493	94854	3	94288
4.0	3.066537	24593	0	24520
5.0	3.529228	11173	0	11165
6.0	3.910807	6206	0	6204
7.0	4.225493	3790	0	3786
8.0	4.485013	2517	0	2514
9.0	4.699038	1870	0	1875
10.0	4.875543	1358	0	1354
11.0	5.021106	1021	0	1022
12.0	5.141152	920	0	919
13.0	5.240152	700	0	698
14.0	5.321798	611	0	612
15.0	5.38913	525	0	526
16.0	5.444659	436	0	434
17.0	5.490453	368	0	368
18.0	5.52822	300	0	302
19.0	5.559365	248	0	247
20.0	5.585051	263	0	266
21.0	5.606234	214	0	211
22.0	5.623704	207	0	206
23.0	5.63811	182	0	183
24.0	5.649992	152	0	152
25.0	5.65979	131	0	130
26.0	5.667871	121	0	122
27.0	5.674535	114	0	113
28.0	5.680031	114	0	114
29.0	5.684564	95	0	95
30.0	5.688302	102	0	102
31.0	5.691384	97	0	97
32.0	5.693926	74	0	74
33.0	5.696023	73	0	74
34.0	5.697752	65	0	64
35.0	5.699178	58	0	58
36.0	5.700354	54	0	54
37.0	5.701324	48	0	48
38.0	5.702123	51	0	51
39.0	5.702783	37	0	38
40.0	5.703327	45	0	44
41.0	5.703775	42	0	42
42.0	5.704145	45	0	45
43.0	5.704451	43	0	44
44.0	5.704702	40	0	39
45.0	5.70491	33	0	33
46.0	5.705081	34	0	34
47.0	5.705222	31	0	31
48.0	5.705338	30	0	30
49.0	5.705434	26	0	26
50.0	5.705513	18	0	18
51.0	5.705579	26	0	27
52.0	5.705633	28	0	27
53.0	5.705677	29	0	29
54.0	5.705714	26	0	26
55.0	5.705744	11	0	11
56.0	5.705769	26	0	26
57.0	5.705789	15	0	15
58.0	5.705806	14	0	14
59.0	5.70582	20	0	20
60.0	5.705832	12	0	13
61.0	5.705841	19	0	18
62.0	5.705849	15	0	15
63.0	5.705855	16	0	16
64.0	5.705861	5	0	5
65.0	5.705865	17	0	17
66.0	5.705869	11	0	11
67.0	5.705872	9	0	9
68.0	5.705874	9	0	9
69.0	5.705876	13	0	13
70.0	5.705878	13	0	13
71.0	5.705879	11	0	11
72.0	5.70588	10	0	10
73.0	5.705881	6	0	6
74.0	5.705882	12	0	13
75.0	5.705883	11	0	10
76.0	5.705883	6	0	7
77.0	5.705884	13	0	12
78.0	5.705884	11	0	11
79.0	5.705884	9	0	9
80.0	5.705885	4	0	4
81.0	5.705885	11	0	11
82.0	5.705885	8	0	8
83.0	5.705885	14	0	14
84.0	5.705885	7	0	7
85.0	5.705885	6	0	6
86.0	5.705885	4	0	5
87.0	5.705886	9	0	8
88.0	5.705886	3	0	3
89.0	5.705886	5	0	5
90.0	5.705886	2	0	2
91.0	5.705886	4	0	4
92.0	5.705886	6	0	6
93.0	5.705886	4	0	4
94.0	5.705886	13	0	13
95.0	5.705886	5	0	6
96.0	5.705886	8	0	7
97.0	5.705886	6	0	6
98.0	5.705886	3	0	3
99.0	5.705886	12	0	12
100.0	5.705886	3	0	3
101.0	0	7	0	7
102.0	0	6	0	6
103.0	0	6	0	7
104.0	0	4	0	3
105.0	0	5	0	5
106.0	0	7	0	7
107.0	0	3	0	3
108.0	0	4	0	4
109.0	0	3	0	3
110.0	0	4	0	4
111.0	0	3	0	3
112.0	0	6	0	6
113.0	0	3	0	3
114.0	0	5	0	6
115.0	0	4	0	4
116.0	0	6	0	5
117.0	0	2	0	2
118.0	0	3	0	3
119.0	0	4	0	4
120.0	0	1	0	1
121.0	0	3	0	3
122.0	0	2	0	2
123.0	0	4	0	4
124.0	0	7	0	7
125.0	0	6	0	6
127.0	0	4	0	4
128.0	0	3	0	3
129.0	0	3	0	3
130.0	0	3	0	3
131.0	0	1	0	1
132.0	0	3	0	3
133.0	0	1	0	1
134.0	0	1	0	1
136.0	0	2	0	2
137.0	0	4	0	4
138.0	0	2	0	2
139.0	0	1	0	1
141.0	0	3	0	3
143.0	0	2	0	2
145.0	0	2	0	2
146.0	0	2	0	2
147.0	0	1	0	1
148.0	0	2	0	2
150.0	0	1	0	1
152.0	0	1	0	1
153.0	0	5	0	5
154.0	0	3	0	3
156.0	0	1	0	1
157.0	0	2	0	2
158.0	0	2	0	2
159.0	0	1	0	1
161.0	0	1	0	1
162.0	0	1	0	1
163.0	0	1	0	1
164.0	0	1	0	1
165.0	0	1	0	1
166.0	0	3	0	3
167.0	0	1	0	1
171.0	0	1	0	1
172.0	0	3	0	3
173.0	0	2	0	2
174.0	0	2	0	2
175.0	0	2	0	2
176.0	0	5	0	5
177.0	0	3	0	3
179.0	0	1	0	1
180.0	0	1	0	1
182.0	0	1	0	1
183.0	0	1	0	1
184.0	0	2	0	2
186.0	0	1	0	1
191.0	0	1	0	1
192.0	0	1	0	1
193.0	0	1	0	1
194.0	0	2	0	2
196.0	0	1	0	1
198.0	0	1	0	1
200.0	0	2	0	2
203.0	0	1	0	1
206.0	0	2	0	2
207.0	0	1	0	1
208.0	0	1	0	1
209.0	0	1	0	1
211.0	0	1	0	1
212.0	0	2	0	2
215.0	0	1	0	1
220.0	0	2	0	2
221.0	0	2	0	2
223.0	0	1	0	1
225.0	0	1	0	1
227.0	0	1	0	1
228.0	0	1	0	1
235.0	0	1	0	1
237.0	0	1	0	1
239.0	0	1	0	1
240.0	0	3	0	3
241.0	0	1	0	1
243.0	0	1	0	1
244.0	0	1	0	1
245.0	0	1	0	1
246.0	0	2	0	2
248.0	0	1	0	1
251.0	0	1	0	1
253.0	0	2	0	2
255.0	0	1	0	1
258.0	0	1	0	1
260.0	0	2	0	2
261.0	0	1	0	1
265.0	0	1	0	1
267.0	0	1	0	1
271.0	0	1	0	1
282.0	0	1	0	1
285.0	0	2	0	2
290.0	0	1	0	1
298.0	0	1	0	1
307.0	0	1	0	1
310.0	0	1	0	1
320.0	0	1	0	1
329.0	0	1	0	1
332.0	0	0	0	1
333.0	0	2	0	1
336.0	0	0	0	1
337.0	0	1	0	0
344.0	0	1	0	1
351.0	0	1	0	1
356.0	0	1	0	1
366.0	0	1	0	1
369.0	0	1	0	1
379.0	0	1	0	1
381.0	0	1	0	1
388.0	0	1	0	1
405.0	0	1	0	2
406.0	0	1	0	0
448.0	0	1	0	1
449.0	0	1	0	1
459.0	0	2	0	2
460.0	0	1	0	1
469.0	0	1	0	1
476.0	0	0	0	1
477.0	0	1	0	0
541.0	0	0	0	1
543.0	0	1	0	0
605.0	0	1	0	1
625.0	0	1	0	1
661.0	0	1	0	1
700.0	0	1	0	1
703.0	0	0	0	1
704.0	0	1	0	0
710.0	0	1	0	1
741.0	0	1	0	1
762.0	0	0	0	1
763.0	0	1	0	0
769.0	0	1	0	1
893.0	0	1	0	1
963.0	0	1	0	1