## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/scratch/tvdkreeke/GHE_RNAseq/GHE_exp2/results/star/GRCh38-45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02.samtools-coordinate-unsieved.bam] OUTPUT=/scratch/tvdkreeke/GHE_RNAseq/GHE_exp2/results/star/GRCh38-45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02.samtools-coordinate-dupmarked.bam METRICS_FILE=/scratch/tvdkreeke/GHE_RNAseq/GHE_exp2/results/qc/markdup/GRCh38-45942_Exp215_GHEtest_6_S2_IPSC_noRibo_A02.samtools-coordinate.metrics.txt TMP_DIR=[/tmp]    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 FLOW_MODE=false FLOW_QUALITY_SUM_STRATEGY=false USE_END_IN_UNPAIRED_READS=false USE_UNPAIRED_CLIPPED_END=false UNPAIRED_END_UNCERTAINTY=0 FLOW_SKIP_FIRST_N_FLOWS=0 FLOW_Q_IS_KNOWN_END=false FLOW_EFFECTIVE_QUALITY_THRESHOLD=15 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 USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Tue Sep 24 14:38:11 CEST 2024

## 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	0	2364756	1339400	0	0	477670	15468	0.201995	5158617

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.00519	1551635	0	1561769
2.0	1.640761	269578	15013	262989
3.0	2.042626	47984	202	45334
4.0	2.29672	9745	10	9087
5.0	2.457381	2881	1	2753
6.0	2.558965	1298	2	1246
7.0	2.623196	808	0	792
8.0	2.663808	514	1	506
9.0	2.689487	410	0	408
10.0	2.705723	273	0	269
11.0	2.715989	290	0	281
12.0	2.72248	184	0	179
13.0	2.726584	147	0	147
14.0	2.729179	139	0	142
15.0	2.73082	103	0	94
16.0	2.731858	88	0	90
17.0	2.732514	96	0	93
18.0	2.732928	74	0	74
19.0	2.733191	56	0	54
20.0	2.733357	56	0	58
21.0	2.733461	45	0	46
22.0	2.733528	42	0	45
23.0	2.73357	41	0	43
24.0	2.733596	45	0	43
25.0	2.733613	39	0	33
26.0	2.733623	22	0	22
27.0	2.73363	29	0	32
28.0	2.733634	19	0	15
29.0	2.733637	13	0	14
30.0	2.733639	25	0	31
31.0	2.73364	19	0	15
32.0	2.733641	18	0	15
33.0	2.733641	13	0	13
34.0	2.733641	19	0	17
35.0	2.733641	11	0	16
36.0	2.733642	18	0	16
37.0	2.733642	18	0	17
38.0	2.733642	15	0	12
39.0	2.733642	3	0	6
40.0	2.733642	10	0	11
41.0	2.733642	11	0	9
42.0	2.733642	7	0	11
43.0	2.733642	10	0	8
44.0	2.733642	12	0	11
45.0	2.733642	8	0	7
46.0	2.733642	7	0	9
47.0	2.733642	13	0	14
48.0	2.733642	8	0	5
49.0	2.733642	6	0	6
50.0	2.733642	7	0	9
51.0	2.733642	9	0	7
52.0	2.733642	4	0	3
53.0	2.733642	2	0	3
54.0	2.733642	5	0	4
55.0	2.733642	2	0	5
56.0	2.733642	5	0	2
57.0	2.733642	4	0	6
58.0	2.733642	8	0	7
59.0	2.733642	3	0	4
60.0	2.733642	6	0	3
61.0	2.733642	4	0	6
62.0	2.733642	6	0	5
63.0	2.733642	1	0	0
64.0	2.733642	5	0	7
65.0	2.733642	3	0	2
66.0	2.733642	1	0	4
67.0	2.733642	4	0	1
68.0	2.733642	3	0	5
69.0	2.733642	7	0	4
70.0	2.733642	2	0	3
71.0	2.733642	3	0	2
72.0	2.733642	2	0	3
73.0	2.733642	1	0	2
74.0	2.733642	3	0	2
75.0	2.733642	2	0	3
76.0	2.733642	2	0	2
77.0	2.733642	1	0	0
78.0	2.733642	2	0	3
79.0	2.733642	2	0	2
80.0	2.733642	4	0	3
81.0	2.733642	1	0	1
82.0	2.733642	3	0	3
83.0	2.733642	1	0	1
84.0	2.733642	2	0	2
85.0	2.733642	1	0	0
86.0	2.733642	2	0	2
87.0	2.733642	0	0	0
88.0	2.733642	0	0	0
89.0	2.733642	0	0	0
90.0	2.733642	0	0	0
91.0	2.733642	1	0	3
92.0	2.733642	2	0	2
93.0	2.733642	1	0	0
94.0	2.733642	1	0	0
95.0	2.733642	0	0	0
96.0	2.733642	1	0	1
97.0	2.733642	1	0	1
98.0	2.733642	0	0	0
99.0	2.733642	0	0	0
100.0	2.733642	0	0	1
101.0	0	2	0	1
102.0	0	0	0	1
103.0	0	1	0	0
104.0	0	0	0	1
105.0	0	1	0	3
106.0	0	1	0	0
107.0	0	2	0	0
108.0	0	1	0	1
111.0	0	1	0	1
112.0	0	1	0	1
113.0	0	1	0	1
114.0	0	1	0	1
115.0	0	1	0	1
119.0	0	1	0	1
120.0	0	0	0	1
121.0	0	1	0	0
125.0	0	0	0	2
126.0	0	1	0	0
127.0	0	1	0	0
128.0	0	1	0	1
133.0	0	0	0	1
134.0	0	1	0	1
135.0	0	1	0	0
136.0	0	0	0	1
137.0	0	1	0	0
144.0	0	0	0	1
145.0	0	1	0	0
148.0	0	1	0	1
150.0	0	1	0	1
152.0	0	0	0	1
153.0	0	1	0	0
167.0	0	0	0	1
168.0	0	1	0	1
169.0	0	1	0	0
173.0	0	1	0	1
176.0	0	0	0	2
177.0	0	2	0	0
187.0	0	0	0	1
189.0	0	1	0	1
190.0	0	1	0	1
191.0	0	1	0	0
204.0	0	1	0	1
219.0	0	1	0	1
220.0	0	0	0	1
222.0	0	1	0	0
235.0	0	1	0	2
238.0	0	1	0	0
244.0	0	0	0	1
248.0	0	1	0	0
257.0	0	0	0	1
259.0	0	1	0	0
286.0	0	0	0	1
287.0	0	2	0	1
299.0	0	0	0	1
302.0	0	1	0	0
314.0	0	0	0	1
315.0	0	1	0	0
319.0	0	0	0	1
322.0	0	1	0	0
325.0	0	0	0	1
327.0	0	1	0	0
339.0	0	0	0	1
344.0	0	1	0	0
414.0	0	0	0	1
419.0	0	1	0	0
495.0	0	0	0	1
497.0	0	1	0	1
503.0	0	0	0	1
504.0	0	2	0	0