## 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_Day19_supernatant_TA_A62_S5.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/GRCh37-NP_Day19_supernatant_TA_A62_S5.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/GRCh37-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: Tue Aug 31 19:21:12 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	145	18467025	0	0	70	2645321	5539	0.143247	58242937

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000255	13894533	0	13898397
2.0	1.728721	1633564	5533	1630955
3.0	2.259249	211594	3	210613
4.0	2.645622	39706	0	39488
5.0	2.92701	13314	0	13268
6.0	3.13194	7062	0	7063
7.0	3.281186	4439	0	4435
8.0	3.389879	3103	0	3098
9.0	3.469038	2213	0	2216
10.0	3.526688	1670	0	1668
11.0	3.568673	1310	0	1309
12.0	3.59925	1028	0	1029
13.0	3.621519	860	0	859
14.0	3.637737	680	0	679
15.0	3.649548	573	0	573
16.0	3.65815	542	0	541
17.0	3.664414	442	0	442
18.0	3.668977	384	0	385
19.0	3.672299	349	0	348
20.0	3.674719	291	0	293
21.0	3.676482	241	0	240
22.0	3.677765	234	0	234
23.0	3.6787	211	0	210
24.0	3.679381	213	0	214
25.0	3.679876	158	0	157
26.0	3.680237	168	0	168
27.0	3.6805	135	0	135
28.0	3.680692	127	0	128
29.0	3.680831	131	0	130
30.0	3.680933	109	0	111
31.0	3.681007	112	0	111
32.0	3.681061	111	0	111
33.0	3.6811	91	0	90
34.0	3.681128	82	0	84
35.0	3.681149	80	0	79
36.0	3.681164	71	0	70
37.0	3.681175	77	0	77
38.0	3.681184	59	0	59
39.0	3.681189	67	0	67
40.0	3.681194	53	0	53
41.0	3.681197	59	0	61
42.0	3.681199	46	0	44
43.0	3.681201	40	0	40
44.0	3.681202	54	0	55
45.0	3.681203	42	0	42
46.0	3.681203	30	0	29
47.0	3.681204	29	0	29
48.0	3.681204	40	0	40
49.0	3.681204	29	0	30
50.0	3.681205	28	0	27
51.0	3.681205	29	0	30
52.0	3.681205	33	0	32
53.0	3.681205	24	0	25
54.0	3.681205	33	0	32
55.0	3.681205	17	0	17
56.0	3.681205	25	0	25
57.0	3.681205	18	0	18
58.0	3.681205	23	0	24
59.0	3.681205	21	0	20
60.0	3.681205	25	0	25
61.0	3.681205	27	0	27
62.0	3.681205	21	0	21
63.0	3.681205	21	0	22
64.0	3.681205	18	0	17
65.0	3.681205	23	0	23
66.0	3.681205	23	0	23
67.0	3.681205	17	0	17
68.0	3.681205	14	0	14
69.0	3.681205	12	0	12
70.0	3.681205	16	0	16
71.0	3.681205	8	0	8
72.0	3.681205	16	0	16
73.0	3.681205	14	0	14
74.0	3.681205	17	0	17
75.0	3.681205	8	0	8
76.0	3.681205	10	0	10
77.0	3.681205	12	0	12
78.0	3.681205	10	0	10
79.0	3.681205	9	0	9
80.0	3.681205	9	0	9
81.0	3.681205	10	0	10
82.0	3.681205	11	0	11
83.0	3.681205	8	0	8
84.0	3.681205	8	0	9
85.0	3.681205	16	0	15
86.0	3.681205	9	0	10
87.0	3.681205	13	0	12
88.0	3.681205	12	0	12
89.0	3.681205	10	0	11
90.0	3.681205	3	0	3
91.0	3.681205	9	0	8
92.0	3.681205	8	0	8
93.0	3.681205	5	0	5
94.0	3.681205	9	0	9
95.0	3.681205	2	0	2
96.0	3.681205	5	0	5
97.0	3.681205	7	0	7
98.0	3.681205	6	0	6
99.0	3.681205	10	0	10
100.0	3.681205	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	8	0	8
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	5	0	4
118.0	0	3	0	3
119.0	0	6	0	6
120.0	0	2	0	2
121.0	0	4	0	4
122.0	0	3	0	3
123.0	0	5	0	5
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	4	0	4
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	4	0	4
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
179.0	0	1	0	1
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	1	0	2
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