## 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_DMSO_A74_S8.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/hg38-NP_Day12_supernatant_DMSO_A74_S8.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/hg38-NP_Day12_supernatant_DMSO_A74_S8.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 14:01:49 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	233	19735499	0	0	119	3560225	4711	0.180399	47950438

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000193	13693324	0	13696471
2.0	1.662923	2039340	4703	2037315
3.0	2.102048	301288	4	300416
4.0	2.393014	65240	0	65049
5.0	2.585808	24714	0	24679
6.0	2.713554	13192	0	13182
7.0	2.798198	8251	0	8251
8.0	2.854284	5610	0	5605
9.0	2.891446	3943	0	3940
10.0	2.91607	2937	0	2940
11.0	2.932386	2221	0	2213
12.0	2.943197	1720	0	1720
13.0	2.95036	1313	0	1315
14.0	2.955107	1121	0	1122
15.0	2.958252	934	0	930
16.0	2.960336	853	0	855
17.0	2.961717	684	0	684
18.0	2.962631	494	0	493
19.0	2.963238	492	0	493
20.0	2.963639	409	0	407
21.0	2.963905	372	0	372
22.0	2.964082	340	0	341
23.0	2.964199	278	0	279
24.0	2.964276	281	0	279
25.0	2.964327	247	0	248
26.0	2.964361	220	0	220
27.0	2.964384	195	0	194
28.0	2.964399	171	0	172
29.0	2.964409	144	0	144
30.0	2.964415	157	0	160
31.0	2.96442	138	0	134
32.0	2.964423	138	0	138
33.0	2.964424	118	0	118
34.0	2.964426	101	0	101
35.0	2.964427	90	0	90
36.0	2.964427	97	0	97
37.0	2.964427	94	0	95
38.0	2.964428	85	0	84
39.0	2.964428	66	0	66
40.0	2.964428	70	0	70
41.0	2.964428	65	0	66
42.0	2.964428	65	0	64
43.0	2.964428	56	0	56
44.0	2.964428	71	0	72
45.0	2.964428	52	0	52
46.0	2.964428	43	0	42
47.0	2.964428	49	0	49
48.0	2.964428	50	0	51
49.0	2.964428	51	0	52
50.0	2.964428	35	0	33
51.0	2.964428	29	0	30
52.0	2.964428	34	0	33
53.0	2.964428	30	0	30
54.0	2.964428	39	0	39
55.0	2.964428	26	0	26
56.0	2.964428	27	0	27
57.0	2.964428	28	0	28
58.0	2.964428	30	0	30
59.0	2.964428	11	0	11
60.0	2.964428	26	0	26
61.0	2.964428	31	0	31
62.0	2.964428	22	0	22
63.0	2.964428	30	0	30
64.0	2.964428	11	0	11
65.0	2.964428	23	0	23
66.0	2.964428	16	0	16
67.0	2.964428	20	0	20
68.0	2.964428	22	0	22
69.0	2.964428	20	0	20
70.0	2.964428	13	0	13
71.0	2.964428	18	0	18
72.0	2.964428	22	0	22
73.0	2.964428	15	0	16
74.0	2.964428	15	0	14
75.0	2.964428	17	0	17
76.0	2.964428	14	0	15
77.0	2.964428	19	0	18
78.0	2.964428	14	0	15
79.0	2.964428	21	0	20
80.0	2.964428	11	0	11
81.0	2.964428	7	0	7
82.0	2.964428	11	0	12
83.0	2.964428	15	0	14
84.0	2.964428	11	0	11
85.0	2.964428	13	0	13
86.0	2.964428	13	0	13
87.0	2.964428	6	0	6
88.0	2.964428	6	0	6
89.0	2.964428	10	0	10
90.0	2.964428	13	0	13
91.0	2.964428	8	0	8
92.0	2.964428	6	0	6
93.0	2.964428	8	0	8
94.0	2.964428	11	0	11
95.0	2.964428	6	0	6
96.0	2.964428	12	0	12
97.0	2.964428	7	0	7
98.0	2.964428	9	0	9
99.0	2.964428	4	0	4
100.0	2.964428	7	0	7
101.0	0	10	0	10
102.0	0	6	0	6
103.0	0	4	0	4
104.0	0	6	0	6
105.0	0	7	0	7
106.0	0	9	0	9
107.0	0	5	0	6
108.0	0	7	0	6
109.0	0	7	0	7
110.0	0	4	0	4
111.0	0	6	0	6
112.0	0	5	0	5
113.0	0	8	0	8
114.0	0	6	0	6
115.0	0	6	0	6
116.0	0	6	0	6
117.0	0	1	0	1
118.0	0	4	0	4
119.0	0	5	0	5
120.0	0	7	0	8
121.0	0	8	0	7
122.0	0	6	0	6
123.0	0	5	0	5
124.0	0	8	0	8
125.0	0	8	0	8
126.0	0	5	0	5
127.0	0	2	0	2
128.0	0	3	0	3
129.0	0	4	0	4
130.0	0	4	0	4
131.0	0	5	0	5
132.0	0	7	0	7
133.0	0	3	0	3
134.0	0	3	0	3
135.0	0	5	0	5
136.0	0	2	0	2
137.0	0	3	0	3
138.0	0	4	0	5
139.0	0	7	0	6
140.0	0	1	0	1
141.0	0	2	0	2
142.0	0	4	0	4
143.0	0	3	0	3
144.0	0	2	0	2
145.0	0	2	0	2
146.0	0	2	0	2
147.0	0	5	0	5
148.0	0	3	0	3
149.0	0	1	0	2
150.0	0	4	0	3
151.0	0	2	0	2
152.0	0	3	0	3
153.0	0	3	0	3
154.0	0	2	0	2
155.0	0	1	0	1
156.0	0	2	0	2
157.0	0	5	0	5
158.0	0	3	0	4
159.0	0	5	0	4
160.0	0	1	0	1
161.0	0	2	0	2
162.0	0	2	0	2
163.0	0	1	0	1
164.0	0	4	0	4
165.0	0	3	0	3
166.0	0	1	0	1
167.0	0	2	0	2
168.0	0	1	0	1
169.0	0	2	0	3
170.0	0	3	0	2
172.0	0	5	0	5
173.0	0	1	0	1
174.0	0	1	0	1
175.0	0	1	0	1
176.0	0	1	0	1
177.0	0	1	0	1
178.0	0	1	0	1
179.0	0	1	0	1
180.0	0	2	0	2
181.0	0	2	0	2
182.0	0	1	0	1
183.0	0	3	0	3
184.0	0	2	0	2
185.0	0	3	0	3
187.0	0	3	0	3
189.0	0	1	0	1
191.0	0	2	0	2
193.0	0	1	0	1
194.0	0	4	0	4
195.0	0	3	0	3
196.0	0	2	0	2
197.0	0	1	0	1
198.0	0	1	0	2
199.0	0	2	0	1
201.0	0	1	0	1
203.0	0	1	0	1
204.0	0	5	0	5
205.0	0	1	0	1
206.0	0	1	0	1
207.0	0	1	0	1
208.0	0	1	0	1
209.0	0	1	0	1
211.0	0	1	0	1
212.0	0	3	0	3
213.0	0	1	0	1
214.0	0	2	0	2
215.0	0	1	0	1
217.0	0	3	0	3
218.0	0	4	0	4
220.0	0	1	0	1
221.0	0	5	0	5
222.0	0	1	0	1
223.0	0	2	0	2
224.0	0	1	0	1
225.0	0	1	0	1
226.0	0	2	0	2
227.0	0	1	0	1
229.0	0	1	0	1
230.0	0	2	0	2
232.0	0	2	0	2
234.0	0	1	0	1
236.0	0	1	0	1
239.0	0	2	0	2
240.0	0	1	0	1
241.0	0	2	0	3
242.0	0	4	0	3
245.0	0	1	0	1
248.0	0	1	0	1
255.0	0	1	0	1
259.0	0	2	0	2
261.0	0	1	0	1
262.0	0	1	0	1
266.0	0	3	0	3
269.0	0	2	0	2
270.0	0	1	0	1
271.0	0	1	0	1
272.0	0	1	0	1
274.0	0	3	0	3
276.0	0	1	0	1
278.0	0	1	0	1
282.0	0	1	0	1
288.0	0	1	0	1
289.0	0	1	0	1
290.0	0	1	0	1
292.0	0	1	0	1
294.0	0	2	0	2
296.0	0	1	0	1
297.0	0	2	0	2
300.0	0	1	0	1
308.0	0	1	0	1
312.0	0	1	0	1
313.0	0	1	0	1
314.0	0	1	0	1
316.0	0	1	0	2
317.0	0	1	0	0
318.0	0	1	0	1
319.0	0	2	0	2
322.0	0	1	0	1
323.0	0	1	0	1
332.0	0	1	0	1
334.0	0	1	0	1
339.0	0	1	0	1
340.0	0	1	0	1
343.0	0	1	0	1
344.0	0	1	0	1
345.0	0	1	0	1
350.0	0	1	0	1
353.0	0	1	0	1
356.0	0	1	0	1
358.0	0	2	0	2
359.0	0	1	0	1
360.0	0	1	0	1
362.0	0	1	0	1
364.0	0	1	0	1
367.0	0	1	0	1
377.0	0	1	0	1
393.0	0	1	0	1
397.0	0	1	0	1
398.0	0	1	0	1
401.0	0	1	0	1
414.0	0	1	0	1
420.0	0	0	0	1
421.0	0	2	0	1
426.0	0	2	0	2
433.0	0	1	0	1
447.0	0	1	0	1
449.0	0	1	0	1
453.0	0	1	0	1
456.0	0	1	0	1
459.0	0	0	0	1
460.0	0	1	0	0
471.0	0	0	0	1
472.0	0	1	0	0
474.0	0	1	0	1
487.0	0	1	0	1
488.0	0	1	0	1
501.0	0	0	0	1
502.0	0	1	0	0
507.0	0	1	0	1
518.0	0	1	0	1
557.0	0	1	0	1
569.0	0	2	0	2
595.0	0	1	0	1
603.0	0	1	0	1
604.0	0	0	0	1
605.0	0	1	0	0
610.0	0	1	0	1
612.0	0	0	0	1
613.0	0	1	0	0
626.0	0	1	0	1
641.0	0	0	0	1
642.0	0	1	0	0
659.0	0	1	0	1
714.0	0	1	0	1
716.0	0	1	0	1
722.0	0	1	0	1
748.0	0	0	0	1
749.0	0	1	0	0
758.0	0	1	0	1
783.0	0	1	0	1
838.0	0	1	0	1
855.0	0	1	0	1
892.0	0	1	0	1
905.0	0	1	0	1
928.0	0	0	0	1
929.0	0	1	0	0
990.0	0	1	0	1
1004.0	0	1	0	1
1035.0	0	1	0	1
1057.0	0	1	0	1
1358.0	0	1	0	1