## 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_Day1_adherentcells_TA_A66_S11.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/GRCh37-NP_Day1_adherentcells_TA_A66_S11.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/GRCh37-NP_Day1_adherentcells_TA_A66_S11.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 19:17:03 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	246	19904093	0	0	125	2412713	5806	0.121219	75475298

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000255	15744016	0	15748550
2.0	1.768642	1499142	5804	1495576
3.0	2.35891	166796	1	165970
4.0	2.812349	36162	0	36061
5.0	3.160677	14554	0	14529
6.0	3.428259	7676	0	7670
7.0	3.633813	4949	0	4945
8.0	3.791718	3289	0	3289
9.0	3.913019	2424	0	2424
10.0	4.006202	1788	0	1789
11.0	4.077784	1353	0	1351
12.0	4.132773	1070	0	1069
13.0	4.175015	892	0	891
14.0	4.207464	717	0	715
15.0	4.232392	605	0	606
16.0	4.251541	515	0	514
17.0	4.266251	454	0	453
18.0	4.277552	396	0	397
19.0	4.286232	334	0	335
20.0	4.292901	306	0	306
21.0	4.298024	260	0	259
22.0	4.301959	253	0	253
23.0	4.304982	221	0	222
24.0	4.307304	199	0	197
25.0	4.309088	155	0	157
26.0	4.310458	157	0	156
27.0	4.311511	143	0	143
28.0	4.31232	137	0	137
29.0	4.312941	107	0	108
30.0	4.313418	135	0	133
31.0	4.313785	103	0	104
32.0	4.314066	83	0	83
33.0	4.314283	87	0	87
34.0	4.314449	74	0	74
35.0	4.314577	76	0	75
36.0	4.314675	72	0	72
37.0	4.31475	65	0	65
38.0	4.314808	69	0	69
39.0	4.314852	53	0	53
40.0	4.314886	61	0	62
41.0	4.314913	58	0	58
42.0	4.314933	48	0	48
43.0	4.314948	45	0	46
44.0	4.31496	52	0	50
45.0	4.314969	35	0	35
46.0	4.314976	45	0	45
47.0	4.314982	39	0	40
48.0	4.314986	36	0	35
49.0	4.314989	47	0	47
50.0	4.314992	28	0	28
51.0	4.314993	27	0	27
52.0	4.314995	24	0	24
53.0	4.314996	37	0	37
54.0	4.314997	23	0	23
55.0	4.314997	22	0	22
56.0	4.314998	24	0	24
57.0	4.314998	26	0	26
58.0	4.314999	34	0	34
59.0	4.314999	21	0	21
60.0	4.314999	21	0	21
61.0	4.314999	16	0	16
62.0	4.314999	22	0	22
63.0	4.314999	13	0	13
64.0	4.314999	12	0	12
65.0	4.314999	23	0	23
66.0	4.314999	17	0	17
67.0	4.315	11	0	11
68.0	4.315	10	0	10
69.0	4.315	14	0	14
70.0	4.315	13	0	13
71.0	4.315	18	0	18
72.0	4.315	16	0	16
73.0	4.315	7	0	7
74.0	4.315	8	0	8
75.0	4.315	7	0	7
76.0	4.315	11	0	11
77.0	4.315	13	0	13
78.0	4.315	11	0	12
79.0	4.315	15	0	14
80.0	4.315	12	0	12
81.0	4.315	11	0	11
82.0	4.315	6	0	6
83.0	4.315	6	0	6
84.0	4.315	6	0	6
85.0	4.315	5	0	5
86.0	4.315	6	0	6
87.0	4.315	7	0	7
88.0	4.315	5	0	5
89.0	4.315	5	0	5
90.0	4.315	6	0	6
91.0	4.315	7	0	7
92.0	4.315	5	0	6
93.0	4.315	9	0	8
94.0	4.315	7	0	7
95.0	4.315	5	0	5
96.0	4.315	6	0	6
97.0	4.315	7	0	7
98.0	4.315	7	0	7
99.0	4.315	4	0	4
100.0	4.315	1	0	1
101.0	0	6	0	7
102.0	0	7	0	6
103.0	0	8	0	8
104.0	0	8	0	9
105.0	0	7	0	6
106.0	0	3	0	3
107.0	0	5	0	5
108.0	0	3	0	3
109.0	0	6	0	6
110.0	0	11	0	11
111.0	0	4	0	4
112.0	0	3	0	3
113.0	0	4	0	4
114.0	0	3	0	3
115.0	0	3	0	3
116.0	0	5	0	5
117.0	0	2	0	2
118.0	0	1	0	1
120.0	0	3	0	3
121.0	0	3	0	5
122.0	0	6	0	4
123.0	0	4	0	5
124.0	0	4	0	3
125.0	0	5	0	5
126.0	0	4	0	4
127.0	0	3	0	3
128.0	0	2	0	2
129.0	0	2	0	2
130.0	0	2	0	2
131.0	0	2	0	2
132.0	0	4	0	4
133.0	0	1	0	1
134.0	0	6	0	6
135.0	0	3	0	3
136.0	0	1	0	2
137.0	0	3	0	2
138.0	0	4	0	5
139.0	0	3	0	2
140.0	0	1	0	1
141.0	0	3	0	3
142.0	0	4	0	4
143.0	0	4	0	4
144.0	0	2	0	2
145.0	0	5	0	5
146.0	0	3	0	3
147.0	0	1	0	1
148.0	0	2	0	2
149.0	0	4	0	4
150.0	0	1	0	1
151.0	0	1	0	1
152.0	0	4	0	4
154.0	0	1	0	1
155.0	0	1	0	1
157.0	0	1	0	1
159.0	0	2	0	2
160.0	0	1	0	1
161.0	0	1	0	1
162.0	0	2	0	2
163.0	0	1	0	1
164.0	0	1	0	1
165.0	0	1	0	1
166.0	0	1	0	1
168.0	0	1	0	1
169.0	0	1	0	1
170.0	0	3	0	3
171.0	0	1	0	1
172.0	0	1	0	1
173.0	0	1	0	1
174.0	0	1	0	1
175.0	0	1	0	1
176.0	0	3	0	3
177.0	0	2	0	2
179.0	0	1	0	1
180.0	0	1	0	1
181.0	0	3	0	3
184.0	0	2	0	2
185.0	0	0	0	1
186.0	0	4	0	3
188.0	0	2	0	2
189.0	0	1	0	1
191.0	0	1	0	1
193.0	0	1	0	1
194.0	0	1	0	1
195.0	0	2	0	2
196.0	0	1	0	1
197.0	0	1	0	1
199.0	0	1	0	1
200.0	0	2	0	2
201.0	0	2	0	2
202.0	0	2	0	2
203.0	0	1	0	1
204.0	0	1	0	1
206.0	0	3	0	3
208.0	0	1	0	2
209.0	0	1	0	0
210.0	0	1	0	1
211.0	0	1	0	1
212.0	0	1	0	1
215.0	0	1	0	1
216.0	0	1	0	1
220.0	0	1	0	1
222.0	0	2	0	2
224.0	0	2	0	2
225.0	0	3	0	3
228.0	0	1	0	1
230.0	0	1	0	1
233.0	0	2	0	2
235.0	0	1	0	1
238.0	0	1	0	1
239.0	0	1	0	1
241.0	0	1	0	1
242.0	0	1	0	1
244.0	0	1	0	1
245.0	0	2	0	3
246.0	0	1	0	0
248.0	0	0	0	1
249.0	0	2	0	2
250.0	0	2	0	1
251.0	0	0	0	1
252.0	0	2	0	1
254.0	0	2	0	2
255.0	0	2	0	2
256.0	0	1	0	1
258.0	0	1	0	2
259.0	0	2	0	1
263.0	0	1	0	1
264.0	0	1	0	1
265.0	0	1	0	1
267.0	0	1	0	1
270.0	0	2	0	2
271.0	0	1	0	1
272.0	0	1	0	1
278.0	0	1	0	1
279.0	0	1	0	1
281.0	0	1	0	1
284.0	0	1	0	1
285.0	0	1	0	1
286.0	0	1	0	1
295.0	0	1	0	1
297.0	0	1	0	1
300.0	0	1	0	1
310.0	0	1	0	1
317.0	0	1	0	1
319.0	0	1	0	1
326.0	0	0	0	1
327.0	0	2	0	1
338.0	0	1	0	1
371.0	0	0	0	1
372.0	0	1	0	0
378.0	0	1	0	1
381.0	0	0	0	1
382.0	0	1	0	0
386.0	0	1	0	1
389.0	0	1	0	1
393.0	0	1	0	1
399.0	0	2	0	2
417.0	0	1	0	1
419.0	0	0	0	1
420.0	0	1	0	0
438.0	0	1	0	1
448.0	0	1	0	1
452.0	0	1	0	1
454.0	0	0	0	1
455.0	0	1	0	0
463.0	0	1	0	1
468.0	0	0	0	1
469.0	0	1	0	0
476.0	0	1	0	1
502.0	0	1	0	1
504.0	0	1	0	1
519.0	0	1	0	1
533.0	0	0	0	1
534.0	0	1	0	0
547.0	0	1	0	1
550.0	0	0	0	1
551.0	0	1	0	0
658.0	0	1	0	1
663.0	0	1	0	1
667.0	0	0	0	1
668.0	0	1	0	1
669.0	0	1	0	0
688.0	0	1	0	1
711.0	0	0	0	1
712.0	0	1	0	0
798.0	0	1	0	1
799.0	0	1	0	1
804.0	0	1	0	1
816.0	0	0	0	1
817.0	0	1	0	0
907.0	0	1	0	1
931.0	0	1	0	1