## 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_DMSO_A72_S3.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/hg38-NP_Day10_supernatant_DMSO_A72_S3.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/hg38-NP_Day10_supernatant_DMSO_A72_S3.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 14:09:10 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	289	16768487	0	0	139	3806754	5041	0.227021	31129533

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000227	10228885	0	10231726
2.0	1.583884	2159690	5025	2158300
3.0	1.924463	426673	8	425707
4.0	2.123199	87958	0	87618
5.0	2.239166	23519	0	23405
6.0	2.306836	9285	0	9267
7.0	2.346323	5086	0	5080
8.0	2.369365	3215	0	3212
9.0	2.382811	2320	0	2320
10.0	2.390656	1735	0	1733
11.0	2.395234	1298	0	1302
12.0	2.397906	1081	0	1078
13.0	2.399465	856	0	855
14.0	2.400374	720	0	719
15.0	2.400905	606	0	608
16.0	2.401215	495	0	492
17.0	2.401396	418	0	418
18.0	2.401501	374	0	374
19.0	2.401563	329	0	330
20.0	2.401599	295	0	295
21.0	2.40162	284	0	283
22.0	2.401632	234	0	234
23.0	2.401639	223	0	223
24.0	2.401643	214	0	214
25.0	2.401646	194	0	194
26.0	2.401647	163	0	163
27.0	2.401648	152	0	155
28.0	2.401648	135	0	133
29.0	2.401649	135	0	134
30.0	2.401649	125	0	126
31.0	2.401649	111	0	111
32.0	2.401649	99	0	99
33.0	2.401649	97	0	96
34.0	2.401649	94	0	94
35.0	2.401649	59	0	60
36.0	2.401649	77	0	77
37.0	2.401649	65	0	64
38.0	2.401649	63	0	64
39.0	2.401649	49	0	49
40.0	2.401649	74	0	73
41.0	2.401649	51	0	52
42.0	2.401649	75	0	74
43.0	2.401649	48	0	48
44.0	2.401649	54	0	54
45.0	2.401649	44	0	44
46.0	2.401649	32	0	32
47.0	2.401649	35	0	35
48.0	2.401649	38	0	38
49.0	2.401649	31	0	33
50.0	2.401649	41	0	39
51.0	2.401649	36	0	36
52.0	2.401649	21	0	21
53.0	2.401649	27	0	29
54.0	2.401649	33	0	32
55.0	2.401649	36	0	36
56.0	2.401649	28	0	28
57.0	2.401649	28	0	28
58.0	2.401649	25	0	24
59.0	2.401649	29	0	29
60.0	2.401649	20	0	20
61.0	2.401649	16	0	18
62.0	2.401649	22	0	20
63.0	2.401649	25	0	25
64.0	2.401649	15	0	16
65.0	2.401649	20	0	19
66.0	2.401649	18	0	18
67.0	2.401649	10	0	11
68.0	2.401649	19	0	18
69.0	2.401649	19	0	19
70.0	2.401649	13	0	13
71.0	2.401649	16	0	16
72.0	2.401649	12	0	12
73.0	2.401649	11	0	11
74.0	2.401649	9	0	9
75.0	2.401649	15	0	15
76.0	2.401649	16	0	17
77.0	2.401649	8	0	7
78.0	2.401649	13	0	13
79.0	2.401649	15	0	15
80.0	2.401649	9	0	9
81.0	2.401649	18	0	18
82.0	2.401649	16	0	17
83.0	2.401649	13	0	12
84.0	2.401649	17	0	17
85.0	2.401649	10	0	10
86.0	2.401649	10	0	10
87.0	2.401649	8	0	9
88.0	2.401649	9	0	8
89.0	2.401649	7	0	7
90.0	2.401649	10	0	10
91.0	2.401649	3	0	3
92.0	2.401649	6	0	7
93.0	2.401649	9	0	9
94.0	2.401649	10	0	9
95.0	2.401649	6	0	7
96.0	2.401649	4	0	4
97.0	2.401649	5	0	5
98.0	2.401649	6	0	5
99.0	2.401649	8	0	8
100.0	2.401649	5	0	5
101.0	0	7	0	7
102.0	0	4	0	4
103.0	0	10	0	10
104.0	0	6	0	6
105.0	0	3	0	3
106.0	0	10	0	10
107.0	0	7	0	8
108.0	0	6	0	5
109.0	0	6	0	6
110.0	0	5	0	5
111.0	0	12	0	12
112.0	0	10	0	10
113.0	0	6	0	6
114.0	0	5	0	5
115.0	0	7	0	7
116.0	0	7	0	7
117.0	0	1	0	1
118.0	0	6	0	6
119.0	0	4	0	5
120.0	0	6	0	5
121.0	0	2	0	2
122.0	0	6	0	6
123.0	0	2	0	2
125.0	0	2	0	2
126.0	0	2	0	2
127.0	0	4	0	4
128.0	0	2	0	2
129.0	0	3	0	3
130.0	0	2	0	2
131.0	0	3	0	3
132.0	0	4	0	4
133.0	0	4	0	4
134.0	0	5	0	5
135.0	0	2	0	2
136.0	0	2	0	2
137.0	0	3	0	3
138.0	0	1	0	1
139.0	0	1	0	1
140.0	0	1	0	1
143.0	0	3	0	3
144.0	0	3	0	3
145.0	0	6	0	6
146.0	0	3	0	3
147.0	0	1	0	1
148.0	0	2	0	2
149.0	0	3	0	3
150.0	0	4	0	4
151.0	0	1	0	1
152.0	0	2	0	2
153.0	0	1	0	1
154.0	0	3	0	3
155.0	0	2	0	2
156.0	0	1	0	1
157.0	0	1	0	1
158.0	0	4	0	4
160.0	0	3	0	4
161.0	0	5	0	4
162.0	0	1	0	1
163.0	0	1	0	1
164.0	0	4	0	4
165.0	0	1	0	1
166.0	0	2	0	2
167.0	0	1	0	1
168.0	0	3	0	3
170.0	0	2	0	3
171.0	0	1	0	0
172.0	0	3	0	3
174.0	0	1	0	1
175.0	0	6	0	6
176.0	0	4	0	4
177.0	0	4	0	4
178.0	0	1	0	1
179.0	0	2	0	2
180.0	0	2	0	2
181.0	0	1	0	1
182.0	0	1	0	1
183.0	0	1	0	1
184.0	0	1	0	1
185.0	0	2	0	2
186.0	0	2	0	2
187.0	0	3	0	3
188.0	0	1	0	1
189.0	0	1	0	1
191.0	0	2	0	2
193.0	0	4	0	4
194.0	0	3	0	3
195.0	0	2	0	2
196.0	0	2	0	2
198.0	0	2	0	2
199.0	0	1	0	1
200.0	0	1	0	1
202.0	0	1	0	1
203.0	0	2	0	2
204.0	0	3	0	3
206.0	0	2	0	2
207.0	0	1	0	1
208.0	0	1	0	1
210.0	0	0	0	1
211.0	0	1	0	0
212.0	0	1	0	1
213.0	0	1	0	1
214.0	0	1	0	1
215.0	0	1	0	1
216.0	0	1	0	1
219.0	0	1	0	1
220.0	0	2	0	2
221.0	0	2	0	2
222.0	0	3	0	3
224.0	0	1	0	1
226.0	0	1	0	1
228.0	0	1	0	1
229.0	0	2	0	2
233.0	0	1	0	1
236.0	0	0	0	1
237.0	0	2	0	1
240.0	0	1	0	1
241.0	0	2	0	2
243.0	0	1	0	1
244.0	0	1	0	1
245.0	0	2	0	2
247.0	0	2	0	2
248.0	0	2	0	2
250.0	0	2	0	2
252.0	0	1	0	1
257.0	0	1	0	1
258.0	0	2	0	2
260.0	0	1	0	1
261.0	0	2	0	2
262.0	0	0	0	2
263.0	0	1	0	0
264.0	0	1	0	0
270.0	0	2	0	2
275.0	0	1	0	1
284.0	0	1	0	1
286.0	0	1	0	1
287.0	0	1	0	1
290.0	0	1	0	1
291.0	0	1	0	1
296.0	0	1	0	1
298.0	0	1	0	1
300.0	0	1	0	1
302.0	0	1	0	1
312.0	0	1	0	1
317.0	0	2	0	2
320.0	0	1	0	1
326.0	0	1	0	1
327.0	0	1	0	1
328.0	0	1	0	1
341.0	0	1	0	1
370.0	0	1	0	1
373.0	0	1	0	1
388.0	0	1	0	1
389.0	0	1	0	1
393.0	0	1	0	1
398.0	0	1	0	1
431.0	0	1	0	1
438.0	0	1	0	1
442.0	0	1	0	1
456.0	0	1	0	1
462.0	0	1	0	1
483.0	0	1	0	1
487.0	0	1	0	1
488.0	0	1	0	1
554.0	0	1	0	1
563.0	0	1	0	1
571.0	0	1	0	1
595.0	0	2	0	2
612.0	0	1	0	1
635.0	0	1	0	1
645.0	0	1	0	1
658.0	0	1	0	1
704.0	0	1	0	1
713.0	0	1	0	1
722.0	0	1	0	1
821.0	0	1	0	1
941.0	0	1	0	1
1033.0	0	1	0	1