## 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_adherent_TA_A64_S1.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/hg38-NP_Day19_adherent_TA_A64_S1.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/hg38-NP_Day19_adherent_TA_A64_S1.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 14:11:27 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	106	16386698	0	0	50	6134534	3651	0.374361	15996313

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000128	6392174	0	6393376
2.0	1.359184	2531218	3641	2531226
3.0	1.488089	894980	5	894477
4.0	1.534367	284530	0	284132
5.0	1.550981	86448	0	86263
6.0	1.556946	27569	0	27480
7.0	1.559087	10717	0	10691
8.0	1.559856	5413	0	5411
9.0	1.560132	3294	0	3291
10.0	1.560231	2299	0	2295
11.0	1.560267	1781	0	1784
12.0	1.560279	1275	0	1274
13.0	1.560284	1049	0	1048
14.0	1.560286	824	0	823
15.0	1.560286	668	0	670
16.0	1.560286	521	0	522
17.0	1.560286	468	0	465
18.0	1.560286	408	0	409
19.0	1.560286	357	0	356
20.0	1.560286	356	0	359
21.0	1.560286	267	0	264
22.0	1.560286	236	0	237
23.0	1.560286	235	0	234
24.0	1.560286	202	0	202
25.0	1.560286	188	0	191
26.0	1.560286	160	0	157
27.0	1.560286	161	0	162
28.0	1.560286	147	0	146
29.0	1.560286	128	0	128
30.0	1.560286	113	0	114
31.0	1.560286	105	0	105
32.0	1.560286	87	0	86
33.0	1.560286	99	0	100
34.0	1.560286	87	0	86
35.0	1.560286	83	0	83
36.0	1.560286	76	0	76
37.0	1.560286	60	0	61
38.0	1.560286	72	0	72
39.0	1.560286	71	0	70
40.0	1.560286	66	0	66
41.0	1.560286	54	0	54
42.0	1.560286	60	0	60
43.0	1.560286	53	0	53
44.0	1.560286	45	0	45
45.0	1.560286	41	0	41
46.0	1.560286	50	0	50
47.0	1.560286	36	0	37
48.0	1.560286	40	0	39
49.0	1.560286	31	0	31
50.0	1.560286	28	0	29
51.0	1.560286	32	0	31
52.0	1.560286	35	0	35
53.0	1.560286	33	0	33
54.0	1.560286	18	0	19
55.0	1.560286	22	0	21
56.0	1.560286	22	0	23
57.0	1.560286	35	0	34
58.0	1.560286	22	0	22
59.0	1.560286	26	0	26
60.0	1.560286	31	0	31
61.0	1.560286	15	0	15
62.0	1.560286	20	0	20
63.0	1.560286	25	0	26
64.0	1.560286	21	0	20
65.0	1.560286	23	0	23
66.0	1.560286	20	0	20
67.0	1.560286	15	0	15
68.0	1.560286	13	0	13
69.0	1.560286	15	0	15
70.0	1.560286	18	0	19
71.0	1.560286	15	0	14
72.0	1.560286	16	0	16
73.0	1.560286	11	0	11
74.0	1.560286	16	0	16
75.0	1.560286	12	0	12
76.0	1.560286	10	0	10
77.0	1.560286	16	0	16
78.0	1.560286	13	0	14
79.0	1.560286	15	0	14
80.0	1.560286	11	0	12
81.0	1.560286	10	0	9
82.0	1.560286	5	0	5
83.0	1.560286	10	0	10
84.0	1.560286	15	0	15
85.0	1.560286	14	0	15
86.0	1.560286	9	0	8
87.0	1.560286	11	0	11
88.0	1.560286	7	0	7
89.0	1.560286	11	0	11
90.0	1.560286	4	0	4
91.0	1.560286	10	0	10
92.0	1.560286	7	0	7
93.0	1.560286	11	0	11
94.0	1.560286	5	0	5
95.0	1.560286	11	0	11
96.0	1.560286	13	0	13
97.0	1.560286	5	0	5
98.0	1.560286	6	0	6
99.0	1.560286	9	0	9
100.0	1.560286	9	0	9
101.0	0	5	0	5
102.0	0	7	0	7
103.0	0	4	0	4
104.0	0	5	0	5
105.0	0	4	0	4
106.0	0	5	0	5
107.0	0	3	0	3
108.0	0	5	0	5
109.0	0	6	0	6
110.0	0	3	0	3
111.0	0	4	0	4
112.0	0	7	0	7
113.0	0	3	0	3
114.0	0	4	0	4
115.0	0	6	0	6
116.0	0	3	0	3
117.0	0	6	0	6
118.0	0	4	0	4
119.0	0	2	0	2
120.0	0	3	0	3
122.0	0	4	0	4
123.0	0	7	0	7
124.0	0	1	0	1
125.0	0	2	0	2
126.0	0	4	0	4
127.0	0	2	0	2
128.0	0	5	0	5
129.0	0	4	0	4
130.0	0	5	0	5
131.0	0	2	0	2
132.0	0	3	0	3
133.0	0	2	0	2
134.0	0	4	0	4
135.0	0	6	0	6
136.0	0	1	0	1
137.0	0	3	0	3
138.0	0	2	0	2
139.0	0	3	0	3
140.0	0	1	0	1
141.0	0	6	0	6
142.0	0	3	0	3
143.0	0	6	0	6
144.0	0	3	0	3
145.0	0	3	0	3
146.0	0	4	0	4
148.0	0	5	0	5
149.0	0	4	0	4
150.0	0	2	0	2
151.0	0	2	0	2
152.0	0	1	0	1
153.0	0	4	0	4
154.0	0	1	0	1
155.0	0	1	0	2
156.0	0	2	0	1
157.0	0	3	0	3
158.0	0	2	0	2
159.0	0	3	0	3
160.0	0	4	0	4
161.0	0	2	0	2
162.0	0	5	0	5
164.0	0	6	0	6
165.0	0	2	0	2
166.0	0	4	0	4
167.0	0	2	0	2
168.0	0	1	0	1
169.0	0	3	0	4
170.0	0	4	0	3
171.0	0	1	0	1
172.0	0	4	0	4
174.0	0	2	0	2
175.0	0	3	0	3
176.0	0	1	0	1
177.0	0	1	0	1
178.0	0	2	0	2
181.0	0	2	0	2
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
189.0	0	3	0	3
190.0	0	3	0	3
191.0	0	1	0	1
193.0	0	1	0	1
194.0	0	3	0	3
195.0	0	3	0	3
197.0	0	3	0	3
198.0	0	1	0	1
199.0	0	3	0	3
200.0	0	2	0	2
201.0	0	3	0	3
203.0	0	4	0	4
204.0	0	2	0	2
205.0	0	1	0	1
206.0	0	1	0	1
208.0	0	1	0	1
210.0	0	3	0	3
215.0	0	1	0	1
217.0	0	1	0	1
218.0	0	1	0	1
219.0	0	1	0	1
220.0	0	1	0	1
222.0	0	1	0	1
223.0	0	1	0	1
224.0	0	1	0	1
226.0	0	1	0	2
227.0	0	2	0	1
228.0	0	1	0	1
230.0	0	1	0	1
231.0	0	1	0	1
234.0	0	2	0	2
235.0	0	3	0	3
236.0	0	2	0	2
237.0	0	1	0	1
238.0	0	0	0	1
239.0	0	2	0	1
240.0	0	1	0	1
243.0	0	1	0	1
244.0	0	2	0	2
246.0	0	1	0	1
249.0	0	0	0	1
250.0	0	3	0	2
253.0	0	1	0	1
255.0	0	3	0	3
257.0	0	1	0	1
259.0	0	1	0	1
260.0	0	5	0	5
261.0	0	2	0	2
263.0	0	2	0	2
269.0	0	1	0	1
279.0	0	2	0	2
281.0	0	1	0	1
283.0	0	3	0	3
284.0	0	2	0	2
286.0	0	1	0	1
288.0	0	1	0	1
289.0	0	1	0	1
291.0	0	1	0	1
297.0	0	1	0	1
298.0	0	1	0	1
299.0	0	3	0	3
308.0	0	2	0	2
310.0	0	1	0	1
313.0	0	1	0	1
314.0	0	1	0	1
315.0	0	1	0	1
321.0	0	1	0	1
326.0	0	2	0	2
328.0	0	2	0	2
337.0	0	4	0	4
346.0	0	2	0	3
348.0	0	1	0	0
354.0	0	1	0	1
357.0	0	1	0	1
358.0	0	1	0	1
363.0	0	1	0	1
365.0	0	1	0	1
374.0	0	1	0	1
417.0	0	2	0	2
421.0	0	1	0	1
432.0	0	1	0	1
445.0	0	1	0	1
454.0	0	1	0	1
474.0	0	1	0	1
505.0	0	1	0	1
510.0	0	1	0	1
511.0	0	1	0	1
513.0	0	1	0	2
514.0	0	1	0	0
526.0	0	1	0	1
530.0	0	1	0	1
531.0	0	1	0	1
533.0	0	1	0	1
603.0	0	1	0	1
607.0	0	1	0	1
627.0	0	1	0	1
652.0	0	1	0	1
694.0	0	2	0	2
701.0	0	1	0	1
718.0	0	1	0	1
743.0	0	0	0	1
744.0	0	1	0	0
769.0	0	1	0	1
936.0	0	0	0	1
937.0	0	1	0	0