## 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_Day1_adherentcells_TA_A66_S11.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/hg38-NP_Day1_adherentcells_TA_A66_S11.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/hg38-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: Mon Aug 30 14:02:52 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	232	19755632	0	0	110	2324108	5765	0.117645	77403304

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000256	15700319	0	15704845
2.0	1.775193	1490644	5763	1487080
3.0	2.375567	163364	1	162544
4.0	2.840699	34256	0	34154
5.0	3.201055	13327	0	13299
6.0	3.480236	6822	0	6816
7.0	3.696529	4319	0	4318
8.0	3.864099	2810	0	2810
9.0	3.993922	2035	0	2035
10.0	4.094501	1485	0	1482
11.0	4.172424	1081	0	1082
12.0	4.232793	870	0	869
13.0	4.279564	716	0	715
14.0	4.315799	596	0	596
15.0	4.343871	471	0	472
16.0	4.36562	442	0	441
17.0	4.38247	348	0	347
18.0	4.395524	315	0	316
19.0	4.405638	252	0	251
20.0	4.413473	236	0	237
21.0	4.419543	195	0	195
22.0	4.424246	196	0	196
23.0	4.42789	185	0	186
24.0	4.430713	149	0	147
25.0	4.432899	129	0	131
26.0	4.434594	135	0	135
27.0	4.435906	112	0	111
28.0	4.436923	118	0	118
29.0	4.437711	88	0	89
30.0	4.438322	108	0	106
31.0	4.438795	82	0	83
32.0	4.439161	57	0	57
33.0	4.439445	68	0	68
34.0	4.439665	62	0	62
35.0	4.439835	59	0	58
36.0	4.439967	59	0	59
37.0	4.440069	52	0	52
38.0	4.440148	44	0	44
39.0	4.44021	45	0	45
40.0	4.440257	44	0	45
41.0	4.440294	41	0	40
42.0	4.440323	35	0	35
43.0	4.440345	41	0	43
44.0	4.440362	39	0	37
45.0	4.440375	28	0	28
46.0	4.440386	33	0	33
47.0	4.440394	32	0	33
48.0	4.4404	29	0	28
49.0	4.440404	38	0	38
50.0	4.440408	25	0	25
51.0	4.440411	19	0	19
52.0	4.440413	20	0	20
53.0	4.440415	31	0	31
54.0	4.440416	18	0	18
55.0	4.440417	22	0	22
56.0	4.440418	19	0	19
57.0	4.440419	20	0	20
58.0	4.440419	24	0	24
59.0	4.44042	13	0	13
60.0	4.44042	14	0	14
61.0	4.44042	12	0	12
62.0	4.44042	20	0	20
63.0	4.44042	12	0	12
64.0	4.440421	11	0	11
65.0	4.440421	19	0	19
66.0	4.440421	12	0	12
67.0	4.440421	10	0	10
68.0	4.440421	7	0	7
69.0	4.440421	11	0	11
70.0	4.440421	13	0	13
71.0	4.440421	16	0	16
72.0	4.440421	14	0	14
73.0	4.440421	5	0	5
74.0	4.440421	8	0	8
75.0	4.440421	7	0	7
76.0	4.440421	8	0	8
77.0	4.440421	10	0	10
78.0	4.440421	8	0	9
79.0	4.440421	14	0	13
80.0	4.440421	10	0	10
81.0	4.440421	9	0	9
82.0	4.440421	6	0	6
83.0	4.440421	5	0	5
84.0	4.440421	5	0	5
85.0	4.440421	5	0	5
86.0	4.440421	4	0	4
87.0	4.440421	7	0	7
88.0	4.440421	4	0	4
89.0	4.440421	5	0	5
90.0	4.440421	6	0	6
91.0	4.440421	6	0	6
92.0	4.440421	4	0	5
93.0	4.440421	7	0	6
94.0	4.440421	6	0	6
95.0	4.440421	4	0	4
96.0	4.440421	5	0	5
97.0	4.440421	6	0	6
98.0	4.440421	7	0	7
99.0	4.440421	4	0	4
100.0	4.440421	1	0	1
101.0	0	5	0	6
102.0	0	7	0	6
103.0	0	9	0	9
104.0	0	8	0	9
105.0	0	5	0	4
106.0	0	2	0	2
107.0	0	5	0	5
108.0	0	2	0	2
109.0	0	5	0	5
110.0	0	10	0	10
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	2	0	4
122.0	0	4	0	2
123.0	0	4	0	5
124.0	0	4	0	3
125.0	0	5	0	5
126.0	0	3	0	3
127.0	0	2	0	2
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	5	0	5
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
141.0	0	2	0	2
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	3	0	3
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	1	0	1
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	1	0	1
202.0	0	1	0	1
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