## 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_Day12_supernatant_TA_A73_S10.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/hg38-NP_Day12_supernatant_TA_A73_S10.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/hg38-NP_Day12_supernatant_TA_A73_S10.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 14:09:53 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	271	17320969	0	0	152	2212153	5270	0.127719	62027808

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000264	13635352	0	13639373
2.0	1.756818	1226842	5266	1223760
3.0	2.329041	149885	2	149080
4.0	2.761844	38561	0	38467
5.0	3.089197	17318	0	17300
6.0	3.336791	9853	0	9849
7.0	3.524061	6377	0	6367
8.0	3.665703	4266	0	4266
9.0	3.772834	3091	0	3095
10.0	3.853864	2290	0	2288
11.0	3.915151	1746	0	1739
12.0	3.961505	1341	0	1344
13.0	3.996566	1055	0	1052
14.0	4.023084	911	0	909
15.0	4.043141	872	0	873
16.0	4.058311	683	0	682
17.0	4.069786	529	0	531
18.0	4.078464	496	0	495
19.0	4.085028	377	0	376
20.0	4.089993	321	0	320
21.0	4.093748	308	0	310
22.0	4.096588	255	0	253
23.0	4.098736	247	0	247
24.0	4.100361	242	0	243
25.0	4.10159	201	0	201
26.0	4.102519	193	0	193
27.0	4.103223	175	0	175
28.0	4.103754	165	0	164
29.0	4.104156	149	0	149
30.0	4.104461	122	0	123
31.0	4.104691	119	0	119
32.0	4.104865	120	0	119
33.0	4.104996	107	0	107
34.0	4.105096	90	0	91
35.0	4.105171	85	0	84
36.0	4.105228	84	0	85
37.0	4.105271	87	0	86
38.0	4.105304	63	0	63
39.0	4.105328	59	0	59
40.0	4.105347	62	0	62
41.0	4.105361	52	0	53
42.0	4.105372	56	0	56
43.0	4.10538	45	0	44
44.0	4.105386	42	0	42
45.0	4.105391	46	0	47
46.0	4.105394	49	0	48
47.0	4.105397	40	0	40
48.0	4.105399	35	0	36
49.0	4.1054	34	0	33
50.0	4.105401	34	0	34
51.0	4.105402	42	0	42
52.0	4.105403	33	0	33
53.0	4.105403	28	0	30
54.0	4.105404	33	0	31
55.0	4.105404	23	0	24
56.0	4.105404	30	0	29
57.0	4.105404	22	0	23
58.0	4.105405	29	0	28
59.0	4.105405	17	0	18
60.0	4.105405	24	0	23
61.0	4.105405	26	0	27
62.0	4.105405	23	0	22
63.0	4.105405	14	0	14
64.0	4.105405	24	0	24
65.0	4.105405	26	0	26
66.0	4.105405	10	0	10
67.0	4.105405	11	0	11
68.0	4.105405	14	0	15
69.0	4.105405	17	0	16
70.0	4.105405	13	0	13
71.0	4.105405	16	0	16
72.0	4.105405	12	0	12
73.0	4.105405	14	0	14
74.0	4.105405	10	0	10
75.0	4.105405	10	0	10
76.0	4.105405	15	0	15
77.0	4.105405	9	0	9
78.0	4.105405	11	0	11
79.0	4.105405	10	0	10
80.0	4.105405	12	0	12
81.0	4.105405	15	0	15
82.0	4.105405	14	0	14
83.0	4.105405	10	0	10
84.0	4.105405	6	0	6
85.0	4.105405	5	0	5
86.0	4.105405	8	0	8
87.0	4.105405	7	0	7
88.0	4.105405	9	0	9
89.0	4.105405	9	0	9
90.0	4.105405	8	0	8
91.0	4.105405	5	0	5
92.0	4.105405	13	0	13
93.0	4.105405	10	0	10
94.0	4.105405	15	0	15
95.0	4.105405	8	0	8
96.0	4.105405	4	0	4
97.0	4.105405	4	0	4
98.0	4.105405	6	0	6
99.0	4.105405	6	0	7
100.0	4.105405	9	0	8
101.0	0	7	0	7
102.0	0	9	0	9
103.0	0	4	0	4
104.0	0	5	0	5
105.0	0	6	0	6
106.0	0	7	0	7
107.0	0	5	0	5
108.0	0	5	0	5
109.0	0	6	0	7
110.0	0	8	0	7
111.0	0	8	0	8
112.0	0	3	0	3
113.0	0	3	0	3
114.0	0	6	0	6
115.0	0	4	0	4
116.0	0	4	0	4
117.0	0	8	0	8
118.0	0	10	0	11
119.0	0	5	0	4
120.0	0	9	0	9
121.0	0	2	0	2
122.0	0	5	0	5
123.0	0	3	0	3
124.0	0	2	0	2
125.0	0	4	0	4
126.0	0	4	0	4
127.0	0	4	0	4
128.0	0	4	0	4
129.0	0	3	0	3
130.0	0	5	0	5
131.0	0	4	0	4
132.0	0	3	0	3
133.0	0	5	0	5
134.0	0	4	0	4
135.0	0	4	0	4
136.0	0	2	0	2
137.0	0	2	0	2
139.0	0	1	0	1
140.0	0	2	0	2
141.0	0	3	0	3
142.0	0	2	0	2
143.0	0	3	0	3
144.0	0	1	0	1
145.0	0	5	0	5
146.0	0	3	0	3
147.0	0	1	0	1
148.0	0	1	0	1
149.0	0	1	0	1
151.0	0	1	0	1
152.0	0	1	0	1
153.0	0	4	0	4
154.0	0	1	0	1
155.0	0	2	0	2
157.0	0	1	0	1
158.0	0	1	0	1
159.0	0	2	0	2
160.0	0	4	0	4
162.0	0	0	0	1
163.0	0	4	0	3
165.0	0	1	0	3
166.0	0	3	0	1
168.0	0	1	0	1
169.0	0	1	0	1
170.0	0	1	0	1
171.0	0	2	0	2
172.0	0	1	0	1
173.0	0	2	0	2
174.0	0	1	0	1
175.0	0	2	0	3
176.0	0	3	0	2
177.0	0	2	0	2
178.0	0	1	0	1
180.0	0	2	0	2
181.0	0	3	0	3
183.0	0	4	0	4
187.0	0	1	0	1
188.0	0	2	0	2
191.0	0	2	0	2
192.0	0	3	0	3
193.0	0	3	0	3
194.0	0	2	0	2
195.0	0	1	0	1
197.0	0	2	0	2
202.0	0	1	0	1
203.0	0	3	0	3
204.0	0	2	0	2
206.0	0	2	0	2
207.0	0	1	0	1
208.0	0	1	0	1
210.0	0	2	0	2
211.0	0	1	0	1
214.0	0	1	0	1
218.0	0	2	0	2
219.0	0	3	0	3
222.0	0	1	0	1
223.0	0	1	0	1
224.0	0	2	0	2
225.0	0	1	0	1
229.0	0	2	0	2
232.0	0	1	0	1
233.0	0	2	0	2
234.0	0	1	0	1
237.0	0	1	0	1
241.0	0	0	0	1
242.0	0	2	0	1
249.0	0	1	0	1
250.0	0	1	0	1
251.0	0	1	0	1
253.0	0	2	0	2
255.0	0	2	0	2
258.0	0	1	0	1
265.0	0	0	0	1
266.0	0	1	0	0
270.0	0	1	0	1
273.0	0	1	0	1
275.0	0	1	0	1
277.0	0	1	0	1
278.0	0	1	0	1
283.0	0	1	0	1
284.0	0	1	0	1
285.0	0	1	0	1
286.0	0	1	0	1
289.0	0	1	0	1
290.0	0	2	0	2
291.0	0	1	0	1
294.0	0	1	0	1
305.0	0	1	0	1
309.0	0	1	0	1
314.0	0	2	0	2
315.0	0	1	0	1
317.0	0	1	0	1
320.0	0	1	0	1
327.0	0	1	0	1
330.0	0	1	0	1
332.0	0	1	0	1
336.0	0	1	0	1
345.0	0	1	0	1
348.0	0	1	0	1
349.0	0	1	0	1
350.0	0	0	0	1
351.0	0	1	0	0
357.0	0	1	0	1
358.0	0	2	0	2
359.0	0	1	0	1
362.0	0	1	0	1
363.0	0	2	0	2
364.0	0	2	0	2
366.0	0	1	0	1
368.0	0	1	0	1
375.0	0	3	0	3
378.0	0	1	0	1
387.0	0	1	0	1
408.0	0	2	0	2
422.0	0	1	0	1
424.0	0	1	0	2
425.0	0	1	0	1
426.0	0	1	0	0
437.0	0	1	0	1
454.0	0	1	0	1
456.0	0	1	0	1
460.0	0	1	0	1
463.0	0	1	0	1
469.0	0	1	0	1
479.0	0	1	0	1
483.0	0	1	0	1
494.0	0	1	0	1
521.0	0	1	0	1
537.0	0	0	0	1
538.0	0	1	0	0
562.0	0	2	0	2
606.0	0	1	0	1
612.0	0	1	0	1
621.0	0	1	0	1
622.0	0	1	0	1
709.0	0	1	0	1
712.0	0	1	0	1
717.0	0	1	0	1
753.0	0	1	0	1
780.0	0	1	0	1
800.0	0	1	0	1
903.0	0	1	0	1
906.0	0	0	0	1
907.0	0	1	0	0
1012.0	0	0	0	1
1013.0	0	1	0	0
1039.0	0	1	0	1
1053.0	0	1	0	1