## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=999 INPUT=[/scratch/tvdkreeke/GHE_RNAseq/GHE_exp2/results/star/GRCh38-45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01.samtools-coordinate-unsieved.bam] OUTPUT=/scratch/tvdkreeke/GHE_RNAseq/GHE_exp2/results/star/GRCh38-45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01.samtools-coordinate-dupmarked.bam METRICS_FILE=/scratch/tvdkreeke/GHE_RNAseq/GHE_exp2/results/qc/markdup/GRCh38-45941_Exp215_GHEtest_5_S2_IPSC_noRibo_A01.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 14:37:20 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	2773249	1572700	0	0	605900	21233	0.21848	5522722

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.005941	1745619	0	1759223
2.0	1.614763	334491	20495	325828
3.0	1.983238	64151	301	60613
4.0	2.206249	13245	22	12190
5.0	2.341221	3592	4	3361
6.0	2.422909	1554	6	1513
7.0	2.47235	918	1	880
8.0	2.502272	602	0	595
9.0	2.520382	452	0	457
10.0	2.531343	363	2	359
11.0	2.537976	286	0	281
12.0	2.541991	225	0	221
13.0	2.544421	190	0	180
14.0	2.545892	164	0	179
15.0	2.546782	141	0	124
16.0	2.54732	102	0	106
17.0	2.547646	104	0	109
18.0	2.547844	79	0	72
19.0	2.547963	72	0	73
20.0	2.548035	57	0	53
21.0	2.548079	63	0	68
22.0	2.548106	62	0	58
23.0	2.548122	52	0	51
24.0	2.548131	46	0	43
25.0	2.548137	40	0	43
26.0	2.548141	35	0	29
27.0	2.548143	35	0	41
28.0	2.548144	30	0	27
29.0	2.548145	35	0	34
30.0	2.548145	28	0	30
31.0	2.548146	27	0	25
32.0	2.548146	22	0	19
33.0	2.548146	12	0	14
34.0	2.548146	17	0	17
35.0	2.548146	16	0	19
36.0	2.548146	28	0	23
37.0	2.548146	16	0	17
38.0	2.548146	17	0	19
39.0	2.548146	14	0	15
40.0	2.548146	14	0	13
41.0	2.548146	13	0	15
42.0	2.548146	16	0	9
43.0	2.548146	9	0	10
44.0	2.548146	5	0	7
45.0	2.548146	13	0	12
46.0	2.548146	9	0	8
47.0	2.548146	4	0	5
48.0	2.548146	6	0	10
49.0	2.548146	13	0	10
50.0	2.548146	11	0	11
51.0	2.548146	7	0	5
52.0	2.548146	2	0	3
53.0	2.548146	8	0	5
54.0	2.548146	6	0	8
55.0	2.548146	4	0	5
56.0	2.548146	10	0	9
57.0	2.548146	4	0	6
58.0	2.548146	8	0	10
59.0	2.548146	9	0	7
60.0	2.548146	6	0	3
61.0	2.548146	2	0	1
62.0	2.548146	4	0	8
63.0	2.548146	4	0	4
64.0	2.548146	3	0	2
65.0	2.548146	7	0	6
66.0	2.548146	1	0	2
67.0	2.548146	8	0	6
68.0	2.548146	1	0	2
69.0	2.548146	4	0	6
70.0	2.548146	5	0	2
71.0	2.548146	2	0	3
72.0	2.548146	2	0	3
73.0	2.548146	5	0	2
74.0	2.548146	0	0	2
75.0	2.548146	4	0	4
76.0	2.548146	5	0	3
77.0	2.548146	3	0	5
78.0	2.548146	4	0	6
79.0	2.548146	3	0	2
80.0	2.548146	3	0	2
81.0	2.548146	4	0	3
82.0	2.548146	2	0	3
83.0	2.548146	0	0	1
84.0	2.548146	3	0	2
85.0	2.548146	2	0	2
86.0	2.548146	1	0	1
87.0	2.548146	1	0	2
88.0	2.548146	3	0	1
89.0	2.548146	0	0	0
90.0	2.548146	1	0	2
91.0	2.548146	2	0	0
92.0	2.548146	1	0	2
93.0	2.548146	1	0	2
94.0	2.548146	1	0	2
95.0	2.548146	1	0	2
96.0	2.548146	2	0	1
97.0	2.548146	4	0	2
98.0	2.548146	1	0	0
99.0	2.548146	0	0	1
100.0	2.548146	2	0	1
101.0	0	0	0	2
102.0	0	1	0	1
103.0	0	2	0	1
104.0	0	2	0	5
105.0	0	1	0	0
106.0	0	2	0	0
107.0	0	2	0	3
108.0	0	2	0	3
109.0	0	2	0	0
110.0	0	1	0	0
113.0	0	0	0	1
114.0	0	0	0	1
115.0	0	1	0	0
116.0	0	1	0	0
119.0	0	1	0	1
121.0	0	0	0	1
122.0	0	0	0	2
123.0	0	4	0	2
124.0	0	0	0	2
125.0	0	1	0	0
126.0	0	2	0	0
127.0	0	0	0	1
128.0	0	1	0	0
129.0	0	0	0	1
131.0	0	0	0	2
132.0	0	1	0	0
133.0	0	2	0	1
134.0	0	1	0	1
136.0	0	1	0	0
137.0	0	1	0	1
138.0	0	0	0	1
140.0	0	1	0	0
145.0	0	0	0	1
146.0	0	1	0	0
151.0	0	0	0	1
155.0	0	1	0	0
161.0	0	0	0	1
163.0	0	2	0	2
166.0	0	1	0	1
167.0	0	1	0	1
170.0	0	1	0	1
175.0	0	1	0	0
184.0	0	1	0	1
194.0	0	0	0	1
196.0	0	1	0	0
203.0	0	1	0	1
208.0	0	0	0	1
209.0	0	1	0	1
212.0	0	1	0	0
232.0	0	0	0	1
233.0	0	1	0	0
243.0	0	0	0	1
244.0	0	0	0	1
245.0	0	1	0	0
248.0	0	1	0	2
249.0	0	1	0	0
250.0	0	1	0	0
259.0	0	0	0	1
261.0	0	1	0	0
262.0	0	0	0	1
263.0	0	0	0	1
264.0	0	1	0	0
267.0	0	1	0	0
269.0	0	0	0	1
271.0	0	1	0	0
286.0	0	0	0	1
288.0	0	1	0	0
300.0	0	0	0	1
301.0	0	1	0	0
306.0	0	0	0	1
309.0	0	1	0	0
311.0	0	0	0	1
316.0	0	1	0	0
328.0	0	0	0	1
331.0	0	1	0	0
374.0	0	0	0	1
379.0	0	1	0	0
391.0	0	0	0	1
396.0	0	1	0	0
448.0	0	0	0	1
451.0	0	1	0	0
495.0	0	0	0	1
498.0	0	1	0	0
501.0	0	0	0	1
505.0	0	1	0	0
541.0	0	0	0	1
547.0	0	1	0	0
650.0	0	0	0	1
659.0	0	1	0	0
668.0	0	0	0	1
677.0	0	1	0	0