## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/star/GRCh37-NP_Day12_supernatant_DMSO_A74_S8.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/GRCh37-NP_Day12_supernatant_DMSO_A74_S8.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/GRCh37-NP_Day12_supernatant_DMSO_A74_S8.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: Tue Aug 31 19:16:37 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	233	19791542	0	0	121	3590937	4729	0.18144	47769836

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000193	13711586	0	13714738
2.0	1.661116	2043547	4721	2041522
3.0	2.097851	302879	4	302004
4.0	2.386444	66128	0	65937
5.0	2.577145	25248	0	25212
6.0	2.70316	13608	0	13597
7.0	2.786429	8513	0	8513
8.0	2.841454	5819	0	5814
9.0	2.877813	4113	0	4111
10.0	2.90184	3036	0	3039
11.0	2.917716	2302	0	2293
12.0	2.928208	1819	0	1819
13.0	2.93514	1374	0	1376
14.0	2.939721	1183	0	1184
15.0	2.942748	970	0	966
16.0	2.944748	884	0	886
17.0	2.94607	701	0	701
18.0	2.946944	529	0	528
19.0	2.947521	505	0	506
20.0	2.947902	429	0	427
21.0	2.948154	387	0	387
22.0	2.948321	352	0	353
23.0	2.948431	291	0	292
24.0	2.948504	294	0	292
25.0	2.948552	251	0	252
26.0	2.948583	225	0	225
27.0	2.948604	204	0	203
28.0	2.948618	176	0	177
29.0	2.948627	146	0	146
30.0	2.948633	164	0	167
31.0	2.948637	138	0	134
32.0	2.94864	140	0	140
33.0	2.948642	124	0	124
34.0	2.948643	105	0	105
35.0	2.948644	97	0	97
36.0	2.948644	98	0	98
37.0	2.948645	96	0	97
38.0	2.948645	85	0	84
39.0	2.948645	68	0	68
40.0	2.948645	70	0	70
41.0	2.948645	71	0	72
42.0	2.948645	65	0	64
43.0	2.948645	58	0	58
44.0	2.948645	76	0	77
45.0	2.948645	54	0	54
46.0	2.948645	45	0	44
47.0	2.948645	50	0	50
48.0	2.948645	54	0	56
49.0	2.948645	52	0	52
50.0	2.948645	36	0	34
51.0	2.948645	31	0	32
52.0	2.948645	35	0	34
53.0	2.948645	31	0	31
54.0	2.948645	40	0	40
55.0	2.948645	28	0	28
56.0	2.948645	28	0	28
57.0	2.948645	29	0	29
58.0	2.948645	34	0	34
59.0	2.948645	11	0	11
60.0	2.948645	29	0	29
61.0	2.948645	30	0	30
62.0	2.948645	22	0	22
63.0	2.948645	29	0	29
64.0	2.948645	11	0	11
65.0	2.948645	23	0	23
66.0	2.948645	17	0	17
67.0	2.948645	22	0	22
68.0	2.948645	23	0	23
69.0	2.948645	22	0	22
70.0	2.948645	13	0	13
71.0	2.948645	19	0	19
72.0	2.948645	22	0	22
73.0	2.948645	15	0	16
74.0	2.948645	16	0	15
75.0	2.948645	18	0	18
76.0	2.948645	14	0	15
77.0	2.948645	19	0	18
78.0	2.948645	13	0	14
79.0	2.948645	21	0	20
80.0	2.948645	11	0	11
81.0	2.948645	8	0	8
82.0	2.948645	12	0	13
83.0	2.948645	15	0	14
84.0	2.948645	12	0	12
85.0	2.948645	13	0	13
86.0	2.948645	13	0	13
87.0	2.948645	7	0	7
88.0	2.948645	7	0	7
89.0	2.948645	10	0	10
90.0	2.948645	12	0	12
91.0	2.948645	7	0	7
92.0	2.948645	6	0	6
93.0	2.948645	8	0	8
94.0	2.948645	11	0	11
95.0	2.948645	6	0	6
96.0	2.948645	12	0	12
97.0	2.948645	7	0	7
98.0	2.948645	9	0	9
99.0	2.948645	4	0	4
100.0	2.948645	7	0	7
101.0	0	10	0	10
102.0	0	6	0	6
103.0	0	4	0	4
104.0	0	6	0	6
105.0	0	7	0	7
106.0	0	9	0	9
107.0	0	4	0	5
108.0	0	7	0	6
109.0	0	7	0	7
110.0	0	4	0	4
111.0	0	6	0	6
112.0	0	6	0	6
113.0	0	7	0	7
114.0	0	6	0	6
115.0	0	6	0	6
116.0	0	6	0	6
117.0	0	1	0	1
118.0	0	4	0	4
119.0	0	4	0	4
120.0	0	8	0	9
121.0	0	8	0	7
122.0	0	6	0	6
123.0	0	5	0	5
124.0	0	8	0	8
125.0	0	8	0	8
126.0	0	5	0	5
127.0	0	2	0	2
128.0	0	3	0	3
129.0	0	4	0	4
130.0	0	4	0	4
131.0	0	5	0	5
132.0	0	7	0	7
133.0	0	3	0	3
134.0	0	3	0	3
135.0	0	5	0	5
136.0	0	2	0	2
137.0	0	3	0	3
138.0	0	4	0	5
139.0	0	7	0	6
140.0	0	1	0	1
141.0	0	2	0	2
142.0	0	4	0	4
143.0	0	3	0	3
144.0	0	2	0	2
145.0	0	2	0	2
146.0	0	2	0	2
147.0	0	5	0	5
148.0	0	3	0	3
149.0	0	1	0	2
150.0	0	4	0	3
151.0	0	2	0	2
152.0	0	3	0	3
153.0	0	3	0	3
154.0	0	2	0	2
155.0	0	1	0	1
156.0	0	2	0	2
157.0	0	5	0	5
158.0	0	3	0	4
159.0	0	5	0	4
160.0	0	1	0	1
161.0	0	2	0	2
162.0	0	2	0	2
163.0	0	1	0	1
164.0	0	4	0	4
165.0	0	3	0	3
166.0	0	1	0	1
167.0	0	2	0	2
168.0	0	1	0	1
169.0	0	2	0	3
170.0	0	3	0	2
172.0	0	5	0	5
173.0	0	1	0	1
174.0	0	1	0	1
175.0	0	1	0	1
176.0	0	1	0	1
177.0	0	1	0	1
178.0	0	1	0	1
179.0	0	1	0	1
180.0	0	2	0	2
181.0	0	2	0	2
182.0	0	2	0	2
183.0	0	2	0	2
184.0	0	2	0	2
185.0	0	3	0	3
187.0	0	3	0	3
189.0	0	1	0	1
191.0	0	2	0	2
193.0	0	1	0	1
194.0	0	4	0	4
195.0	0	3	0	3
196.0	0	2	0	2
197.0	0	1	0	1
198.0	0	1	0	2
199.0	0	2	0	1
201.0	0	1	0	1
203.0	0	1	0	1
204.0	0	5	0	5
205.0	0	1	0	1
206.0	0	1	0	1
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	3	0	3
213.0	0	1	0	1
214.0	0	2	0	2
215.0	0	1	0	1
217.0	0	3	0	3
218.0	0	4	0	4
220.0	0	1	0	1
221.0	0	5	0	5
222.0	0	1	0	1
223.0	0	2	0	2
224.0	0	1	0	1
225.0	0	1	0	1
226.0	0	2	0	2
227.0	0	1	0	1
229.0	0	1	0	1
230.0	0	2	0	2
232.0	0	2	0	2
234.0	0	1	0	1
236.0	0	1	0	1
239.0	0	2	0	2
240.0	0	1	0	1
241.0	0	2	0	3
242.0	0	4	0	3
245.0	0	1	0	1
248.0	0	1	0	1
255.0	0	1	0	1
259.0	0	2	0	2
261.0	0	1	0	1
262.0	0	1	0	1
266.0	0	3	0	3
269.0	0	2	0	2
270.0	0	1	0	1
271.0	0	1	0	1
272.0	0	1	0	1
274.0	0	3	0	3
276.0	0	1	0	1
278.0	0	1	0	1
282.0	0	1	0	1
288.0	0	1	0	1
289.0	0	1	0	1
290.0	0	1	0	1
292.0	0	1	0	1
294.0	0	2	0	2
296.0	0	1	0	1
297.0	0	2	0	2
300.0	0	1	0	1
308.0	0	1	0	1
312.0	0	1	0	1
313.0	0	1	0	1
314.0	0	1	0	1
316.0	0	1	0	2
317.0	0	1	0	0
318.0	0	1	0	1
319.0	0	2	0	2
322.0	0	1	0	1
323.0	0	1	0	1
332.0	0	1	0	1
334.0	0	1	0	1
339.0	0	1	0	1
340.0	0	1	0	1
343.0	0	1	0	1
344.0	0	1	0	1
345.0	0	1	0	1
350.0	0	1	0	1
353.0	0	1	0	1
356.0	0	1	0	1
358.0	0	2	0	2
359.0	0	1	0	1
360.0	0	1	0	1
362.0	0	1	0	1
364.0	0	1	0	1
367.0	0	1	0	1
377.0	0	1	0	1
393.0	0	1	0	1
397.0	0	1	0	1
398.0	0	1	0	1
401.0	0	1	0	1
414.0	0	1	0	1
420.0	0	0	0	1
421.0	0	2	0	1
426.0	0	2	0	2
433.0	0	1	0	1
447.0	0	1	0	1
449.0	0	1	0	1
453.0	0	1	0	1
456.0	0	1	0	1
459.0	0	0	0	1
460.0	0	1	0	0
471.0	0	0	0	1
472.0	0	1	0	0
474.0	0	1	0	1
487.0	0	1	0	1
488.0	0	1	0	1
501.0	0	0	0	1
502.0	0	1	0	0
507.0	0	1	0	1
518.0	0	1	0	1
557.0	0	1	0	1
569.0	0	2	0	2
595.0	0	1	0	1
603.0	0	1	0	1
604.0	0	0	0	1
605.0	0	1	0	0
610.0	0	1	0	1
612.0	0	0	0	1
613.0	0	1	0	0
626.0	0	1	0	1
641.0	0	0	0	1
642.0	0	1	0	0
659.0	0	1	0	1
714.0	0	1	0	1
716.0	0	1	0	1
722.0	0	1	0	1
748.0	0	0	0	1
749.0	0	1	0	0
758.0	0	1	0	1
783.0	0	1	0	1
838.0	0	1	0	1
855.0	0	1	0	1
892.0	0	1	0	1
905.0	0	1	0	1
928.0	0	0	0	1
929.0	0	1	0	0
990.0	0	1	0	1
1004.0	0	1	0	1
1035.0	0	1	0	1
1057.0	0	1	0	1
1358.0	0	1	0	1