## 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_Day19_supernatant_TA_A62_S5.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/hg38-NP_Day19_supernatant_TA_A62_S5.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/hg38-NP_Day19_supernatant_TA_A62_S5.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 14:07:23 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	140	18366565	0	0	68	2586789	5514	0.140844	59027017

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000256	13867332	0	13871187
2.0	1.733044	1626381	5508	1623778
3.0	2.269884	208660	3	207678
4.0	2.663173	38078	0	37862
5.0	2.951297	12326	0	12280
6.0	3.162377	6427	0	6429
7.0	3.317014	3935	0	3931
8.0	3.430301	2755	0	2751
9.0	3.513295	1927	0	1929
10.0	3.574096	1456	0	1455
11.0	3.618639	1150	0	1149
12.0	3.651272	871	0	872
13.0	3.675178	759	0	757
14.0	3.692692	585	0	585
15.0	3.705523	495	0	494
16.0	3.714923	470	0	470
17.0	3.721809	385	0	385
18.0	3.726854	341	0	342
19.0	3.73055	310	0	309
20.0	3.733257	257	0	259
21.0	3.735241	206	0	205
22.0	3.736694	207	0	207
23.0	3.737759	190	0	189
24.0	3.738538	183	0	184
25.0	3.73911	136	0	135
26.0	3.739528	152	0	152
27.0	3.739835	113	0	113
28.0	3.74006	103	0	104
29.0	3.740224	114	0	113
30.0	3.740345	105	0	107
31.0	3.740433	106	0	105
32.0	3.740498	102	0	102
33.0	3.740545	83	0	82
34.0	3.74058	73	0	75
35.0	3.740606	74	0	73
36.0	3.740624	65	0	64
37.0	3.740638	72	0	72
38.0	3.740648	53	0	53
39.0	3.740655	63	0	63
40.0	3.740661	47	0	47
41.0	3.740664	50	0	52
42.0	3.740667	41	0	39
43.0	3.740669	35	0	35
44.0	3.740671	48	0	49
45.0	3.740672	37	0	37
46.0	3.740673	27	0	26
47.0	3.740674	28	0	28
48.0	3.740674	36	0	36
49.0	3.740674	28	0	29
50.0	3.740675	27	0	26
51.0	3.740675	25	0	26
52.0	3.740675	30	0	29
53.0	3.740675	20	0	21
54.0	3.740675	29	0	28
55.0	3.740675	16	0	16
56.0	3.740675	23	0	23
57.0	3.740675	16	0	16
58.0	3.740675	23	0	24
59.0	3.740675	21	0	20
60.0	3.740675	24	0	24
61.0	3.740675	26	0	26
62.0	3.740675	21	0	21
63.0	3.740675	20	0	21
64.0	3.740675	18	0	17
65.0	3.740675	22	0	22
66.0	3.740675	23	0	23
67.0	3.740675	17	0	17
68.0	3.740675	14	0	14
69.0	3.740675	12	0	12
70.0	3.740675	16	0	16
71.0	3.740675	9	0	9
72.0	3.740675	13	0	13
73.0	3.740675	13	0	13
74.0	3.740675	16	0	16
75.0	3.740675	8	0	8
76.0	3.740675	10	0	10
77.0	3.740675	12	0	12
78.0	3.740675	10	0	10
79.0	3.740675	9	0	9
80.0	3.740675	9	0	9
81.0	3.740675	9	0	9
82.0	3.740675	11	0	11
83.0	3.740675	8	0	8
84.0	3.740675	8	0	9
85.0	3.740675	15	0	14
86.0	3.740675	8	0	9
87.0	3.740675	12	0	11
88.0	3.740675	10	0	10
89.0	3.740675	9	0	10
90.0	3.740675	3	0	3
91.0	3.740675	9	0	8
92.0	3.740675	8	0	8
93.0	3.740675	5	0	5
94.0	3.740675	9	0	9
95.0	3.740675	2	0	2
96.0	3.740675	5	0	5
97.0	3.740675	7	0	7
98.0	3.740675	6	0	6
99.0	3.740675	9	0	9
100.0	3.740675	4	0	4
101.0	0	7	0	7
102.0	0	8	0	8
103.0	0	9	0	9
104.0	0	6	0	6
105.0	0	7	0	7
106.0	0	6	0	6
107.0	0	8	0	8
108.0	0	1	0	1
109.0	0	1	0	1
110.0	0	1	0	1
111.0	0	3	0	3
112.0	0	4	0	4
113.0	0	4	0	4
114.0	0	6	0	6
115.0	0	3	0	3
116.0	0	1	0	2
117.0	0	4	0	3
118.0	0	3	0	3
119.0	0	5	0	5
120.0	0	2	0	2
121.0	0	4	0	4
122.0	0	3	0	3
123.0	0	4	0	4
124.0	0	5	0	5
125.0	0	4	0	4
126.0	0	2	0	2
127.0	0	7	0	7
128.0	0	5	0	5
129.0	0	5	0	5
130.0	0	2	0	2
131.0	0	5	0	5
132.0	0	2	0	3
133.0	0	2	0	1
134.0	0	1	0	1
135.0	0	3	0	3
136.0	0	3	0	3
137.0	0	3	0	3
138.0	0	1	0	1
139.0	0	4	0	4
140.0	0	1	0	1
141.0	0	2	0	2
142.0	0	4	0	4
143.0	0	2	0	2
144.0	0	2	0	2
145.0	0	2	0	2
146.0	0	3	0	4
147.0	0	5	0	4
148.0	0	3	0	3
149.0	0	4	0	4
150.0	0	3	0	3
151.0	0	2	0	2
152.0	0	3	0	3
153.0	0	3	0	3
154.0	0	1	0	1
155.0	0	1	0	1
156.0	0	1	0	1
157.0	0	1	0	1
158.0	0	1	0	1
159.0	0	4	0	4
160.0	0	2	0	2
161.0	0	5	0	5
162.0	0	4	0	4
163.0	0	1	0	1
164.0	0	3	0	3
165.0	0	1	0	1
166.0	0	3	0	3
167.0	0	1	0	1
168.0	0	1	0	1
169.0	0	2	0	2
170.0	0	4	0	4
171.0	0	1	0	1
173.0	0	2	0	2
175.0	0	2	0	3
176.0	0	1	0	0
180.0	0	2	0	2
181.0	0	1	0	1
182.0	0	3	0	3
183.0	0	3	0	3
184.0	0	2	0	2
185.0	0	1	0	1
186.0	0	1	0	1
187.0	0	2	0	2
188.0	0	1	0	1
189.0	0	1	0	1
190.0	0	1	0	2
191.0	0	1	0	0
192.0	0	1	0	1
193.0	0	2	0	2
194.0	0	1	0	1
195.0	0	1	0	1
196.0	0	1	0	1
197.0	0	1	0	1
198.0	0	0	0	1
199.0	0	1	0	0
200.0	0	5	0	5
201.0	0	2	0	2
202.0	0	3	0	4
203.0	0	1	0	0
204.0	0	1	0	1
205.0	0	2	0	2
206.0	0	5	0	5
207.0	0	1	0	1
208.0	0	5	0	5
209.0	0	1	0	1
211.0	0	2	0	2
212.0	0	1	0	1
213.0	0	2	0	2
214.0	0	1	0	1
215.0	0	2	0	2
216.0	0	1	0	2
217.0	0	1	0	0
218.0	0	1	0	1
219.0	0	2	0	2
220.0	0	3	0	3
221.0	0	2	0	2
223.0	0	1	0	1
224.0	0	1	0	1
228.0	0	2	0	2
229.0	0	1	0	1
232.0	0	2	0	2
235.0	0	2	0	2
237.0	0	1	0	1
238.0	0	1	0	1
239.0	0	2	0	2
240.0	0	1	0	1
241.0	0	1	0	1
242.0	0	1	0	1
243.0	0	2	0	2
244.0	0	1	0	2
246.0	0	1	0	0
251.0	0	1	0	1
253.0	0	1	0	1
256.0	0	1	0	1
260.0	0	0	0	1
261.0	0	2	0	1
262.0	0	1	0	1
270.0	0	1	0	1
274.0	0	1	0	1
276.0	0	2	0	2
277.0	0	2	0	2
279.0	0	1	0	1
280.0	0	1	0	1
283.0	0	1	0	1
284.0	0	1	0	1
285.0	0	1	0	1
293.0	0	1	0	1
297.0	0	1	0	1
304.0	0	1	0	1
308.0	0	1	0	1
318.0	0	1	0	2
319.0	0	1	0	0
322.0	0	1	0	1
325.0	0	1	0	1
333.0	0	1	0	1
335.0	0	1	0	1
336.0	0	1	0	1
343.0	0	1	0	1
348.0	0	1	0	1
351.0	0	1	0	1
354.0	0	1	0	1
359.0	0	1	0	1
365.0	0	1	0	1
370.0	0	1	0	1
371.0	0	1	0	1
379.0	0	1	0	1
390.0	0	0	0	1
391.0	0	1	0	0
401.0	0	1	0	1
419.0	0	1	0	1
423.0	0	1	0	1
446.0	0	1	0	1
467.0	0	1	0	1
470.0	0	0	0	1
471.0	0	1	0	0
490.0	0	3	0	3
495.0	0	1	0	1
499.0	0	1	0	1
510.0	0	1	0	1
529.0	0	1	0	1
564.0	0	1	0	1
596.0	0	1	0	1
601.0	0	0	0	1
603.0	0	1	0	0
655.0	0	1	0	1
689.0	0	1	0	1
720.0	0	2	0	2
721.0	0	1	0	1
749.0	0	1	0	1
762.0	0	1	0	1
842.0	0	1	0	1
859.0	0	1	0	1
926.0	0	1	0	1
1149.0	0	1	0	1
1172.0	0	1	0	1