## 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_adherent_TA_A60_S4.samtools-coordinate-sieved.bam] OUTPUT=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/final_bam/hg38-NP_Day12_adherent_TA_A60_S4.samtools-coordinate.bam METRICS_FILE=/ceph/rimlsfnwi/data/moldevbio/heeringen/siebrenf/ghe_2021/results/qc/markdup/hg38-NP_Day12_adherent_TA_A60_S4.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 14:07:45 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	224	18573011	0	0	144	2705068	6567	0.145648	57519557

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.0003	13881608	0	13886225
2.0	1.724564	1640051	6553	1636839
3.0	2.248965	238523	7	237447
4.0	2.628656	52439	0	52197
5.0	2.90357	19230	0	19172
6.0	3.10262	10179	0	10167
7.0	3.246742	6085	0	6081
8.0	3.351094	3988	0	3979
9.0	3.426649	2795	0	2799
10.0	3.481354	2037	0	2035
11.0	3.520963	1583	0	1583
12.0	3.549642	1123	0	1119
13.0	3.570407	922	0	924
14.0	3.585442	756	0	754
15.0	3.596328	590	0	591
16.0	3.60421	510	0	510
17.0	3.609917	383	0	383
18.0	3.614049	321	0	319
19.0	3.617041	321	0	320
20.0	3.619207	241	0	243
21.0	3.620775	214	0	214
22.0	3.621911	199	0	199
23.0	3.622733	178	0	178
24.0	3.623329	155	0	153
25.0	3.62376	136	0	137
26.0	3.624072	106	0	106
27.0	3.624298	96	0	97
28.0	3.624461	106	0	104
29.0	3.62458	76	0	76
30.0	3.624666	60	0	61
31.0	3.624728	71	0	73
32.0	3.624773	66	0	64
33.0	3.624805	53	0	54
34.0	3.624829	56	0	54
35.0	3.624846	54	0	54
36.0	3.624858	40	0	41
37.0	3.624867	49	0	48
38.0	3.624874	42	0	42
39.0	3.624878	40	0	40
40.0	3.624882	20	0	20
41.0	3.624884	28	0	28
42.0	3.624886	23	0	23
43.0	3.624887	33	0	33
44.0	3.624888	29	0	29
45.0	3.624889	17	0	17
46.0	3.624889	28	0	28
47.0	3.62489	34	0	35
48.0	3.62489	18	0	17
49.0	3.62489	17	0	17
50.0	3.62489	18	0	18
51.0	3.62489	19	0	19
52.0	3.62489	12	0	14
53.0	3.62489	18	0	16
54.0	3.62489	18	0	18
55.0	3.624891	10	0	10
56.0	3.624891	14	0	14
57.0	3.624891	15	0	15
58.0	3.624891	8	0	8
59.0	3.624891	20	0	20
60.0	3.624891	15	0	15
61.0	3.624891	8	0	8
62.0	3.624891	13	0	13
63.0	3.624891	12	0	12
64.0	3.624891	8	0	8
65.0	3.624891	12	0	12
66.0	3.624891	4	0	4
67.0	3.624891	6	0	7
68.0	3.624891	6	0	5
69.0	3.624891	8	0	8
70.0	3.624891	6	0	6
71.0	3.624891	10	0	10
72.0	3.624891	4	0	5
73.0	3.624891	9	0	8
74.0	3.624891	6	0	6
75.0	3.624891	2	0	2
76.0	3.624891	6	0	6
77.0	3.624891	9	0	9
78.0	3.624891	3	0	3
79.0	3.624891	7	0	7
80.0	3.624891	7	0	7
81.0	3.624891	3	0	3
82.0	3.624891	4	0	4
83.0	3.624891	0	0	0
84.0	3.624891	6	0	6
85.0	3.624891	4	0	4
86.0	3.624891	7	0	7
87.0	3.624891	3	0	3
88.0	3.624891	7	0	7
89.0	3.624891	3	0	3
90.0	3.624891	7	0	7
91.0	3.624891	2	0	2
92.0	3.624891	5	0	5
93.0	3.624891	3	0	3
94.0	3.624891	2	0	2
95.0	3.624891	4	0	4
96.0	3.624891	4	0	4
97.0	3.624891	2	0	2
98.0	3.624891	3	0	3
99.0	3.624891	1	0	2
100.0	3.624891	7	0	6
101.0	0	2	0	2
102.0	0	3	0	3
103.0	0	4	0	4
105.0	0	2	0	2
106.0	0	2	0	2
107.0	0	1	0	1
109.0	0	3	0	3
110.0	0	2	0	2
111.0	0	1	0	1
113.0	0	2	0	2
114.0	0	1	0	1
115.0	0	2	0	2
117.0	0	3	0	3
118.0	0	4	0	4
119.0	0	2	0	2
120.0	0	1	0	1
121.0	0	3	0	3
123.0	0	1	0	1
124.0	0	4	0	4
126.0	0	1	0	1
127.0	0	2	0	2
128.0	0	1	0	1
129.0	0	2	0	2
130.0	0	1	0	1
131.0	0	1	0	1
132.0	0	1	0	1
133.0	0	1	0	1
134.0	0	2	0	2
135.0	0	1	0	1
137.0	0	1	0	1
139.0	0	3	0	3
141.0	0	1	0	1
142.0	0	2	0	2
144.0	0	2	0	2
147.0	0	1	0	1
148.0	0	1	0	1
154.0	0	1	0	1
156.0	0	2	0	2
157.0	0	1	0	1
163.0	0	1	0	1
164.0	0	1	0	1
167.0	0	1	0	1
170.0	0	1	0	1
171.0	0	2	0	2
172.0	0	1	0	1
174.0	0	1	0	1
177.0	0	1	0	1
181.0	0	1	0	1
182.0	0	1	0	1
183.0	0	1	0	1
185.0	0	1	0	1
188.0	0	2	0	2
189.0	0	1	0	1
190.0	0	1	0	1
191.0	0	2	0	2
194.0	0	2	0	2
197.0	0	1	0	1
199.0	0	1	0	1
200.0	0	1	0	1
201.0	0	1	0	1
202.0	0	1	0	1
203.0	0	3	0	3
204.0	0	1	0	1
207.0	0	2	0	2
213.0	0	1	0	1
217.0	0	1	0	1
220.0	0	1	0	1
225.0	0	1	0	1
230.0	0	0	0	1
231.0	0	1	0	0
234.0	0	2	0	2
239.0	0	1	0	1
240.0	0	1	0	1
242.0	0	1	0	1
243.0	0	1	0	1
244.0	0	1	0	1
245.0	0	1	0	1
249.0	0	1	0	1
252.0	0	1	0	1
254.0	0	1	0	1
255.0	0	1	0	1
258.0	0	1	0	1
261.0	0	1	0	1
262.0	0	1	0	1
278.0	0	1	0	1
290.0	0	1	0	1
304.0	0	1	0	1
307.0	0	0	0	1
308.0	0	1	0	0
346.0	0	1	0	1
349.0	0	1	0	1
372.0	0	2	0	2
374.0	0	1	0	1
384.0	0	1	0	1
387.0	0	1	0	1
388.0	0	1	0	1
448.0	0	1	0	1
453.0	0	1	0	1
467.0	0	1	0	1
512.0	0	1	0	1
635.0	0	1	0	1
638.0	0	1	0	1
651.0	0	1	0	1