## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/FR_Hau_Civ_1_2018-09-15/FR_Hau_Civ_1_2018-09-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/FR_Hau_Civ_1_2018-09-15/FR_Hau_Civ_1_2018-09-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/FR_Hau_Civ_1_2018-09-15/FR_Hau_Civ_1_2018-09-15.mark_duplicates_report.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT    MAX_SEQUENCES_FOR_DISK_READ_ENDS_MAP=50000 MAX_FILE_HANDLES_FOR_READ_ENDS_MAP=8000 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 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 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: Thu Jan 19 08:22:02 UTC 2023

## 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
lib1	6189981	25044294	0	0	3624398	4103588	222798	0.210232	70869496

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.007484	17072039	0	17231863
2.0	1.715046	2758202	218765	2645654
3.0	2.211971	453812	1994	417920
4.0	2.560964	82556	15	73811
5.0	2.806065	18895	0	17019
6.0	2.9782	6213	0	5728
7.0	3.099091	2791	0	2669
8.0	3.183994	1489	0	1422
9.0	3.243622	948	0	934
10.0	3.285499	639	0	608
11.0	3.31491	453	0	450
12.0	3.335565	331	0	318
13.0	3.350071	214	0	207
14.0	3.360259	183	0	185
15.0	3.367414	127	0	118
16.0	3.372439	118	0	126
17.0	3.375968	96	0	83
18.0	3.378446	82	0	80
19.0	3.380187	70	0	73
20.0	3.38141	63	0	57
21.0	3.382268	54	0	56
22.0	3.382871	53	0	52
23.0	3.383295	31	0	31
24.0	3.383592	27	0	24
25.0	3.383801	20	0	25
26.0	3.383947	31	0	27
27.0	3.38405	20	0	20
28.0	3.384123	16	0	15
29.0	3.384174	13	0	15
30.0	3.384209	15	0	13
31.0	3.384234	14	0	14
32.0	3.384252	9	0	8
33.0	3.384264	11	0	10
34.0	3.384273	15	0	16
35.0	3.384279	13	0	15
36.0	3.384283	11	0	9
37.0	3.384286	9	0	11
38.0	3.384289	9	0	6
39.0	3.38429	5	0	5
40.0	3.384291	6	0	9
41.0	3.384292	11	0	9
42.0	3.384292	6	0	6
43.0	3.384293	6	0	5
44.0	3.384293	5	0	5
45.0	3.384293	4	0	5
46.0	3.384293	6	0	5
47.0	3.384293	1	0	1
48.0	3.384293	2	0	2
49.0	3.384293	5	0	5
50.0	3.384293	3	0	4
51.0	3.384293	2	0	1
52.0	3.384294	2	0	3
53.0	3.384294	5	0	5
54.0	3.384294	3	0	2
55.0	3.384294	0	0	1
56.0	3.384294	3	0	5
57.0	3.384294	3	0	2
58.0	3.384294	5	0	4
59.0	3.384294	1	0	0
60.0	3.384294	2	0	3
61.0	3.384294	2	0	2
62.0	3.384294	4	0	4
63.0	3.384294	3	0	2
64.0	3.384294	3	0	3
65.0	3.384294	1	0	2
66.0	3.384294	2	0	1
67.0	3.384294	2	0	2
68.0	3.384294	0	0	0
69.0	3.384294	1	0	1
70.0	3.384294	1	0	1
71.0	3.384294	0	0	0
72.0	3.384294	1	0	1
73.0	3.384294	0	0	0
74.0	3.384294	1	0	1
75.0	3.384294	0	0	0
76.0	3.384294	3	0	3
77.0	3.384294	0	0	0
78.0	3.384294	1	0	1
79.0	3.384294	0	0	0
80.0	3.384294	1	0	1
81.0	3.384294	0	0	1
82.0	3.384294	3	0	2
83.0	3.384294	1	0	1
84.0	3.384294	0	0	0
85.0	3.384294	2	0	2
86.0	3.384294	1	0	1
87.0	3.384294	0	0	0
88.0	3.384294	0	0	0
89.0	3.384294	0	0	0
90.0	3.384294	0	0	0
91.0	3.384294	0	0	0
92.0	3.384294	1	0	1
93.0	3.384294	1	0	2
94.0	3.384294	1	0	0
95.0	3.384294	0	0	0
96.0	3.384294	0	0	1
97.0	3.384294	1	0	0
98.0	3.384294	0	0	0
99.0	3.384294	0	0	0
100.0	3.384294	1	0	1
101.0	0	1	0	1
104.0	0	1	0	1
107.0	0	1	0	1
110.0	0	1	0	1
111.0	0	0	0	1
112.0	0	2	0	1
115.0	0	0	0	1
116.0	0	1	0	0
117.0	0	1	0	2
118.0	0	1	0	1
119.0	0	1	0	0
121.0	0	0	0	1
122.0	0	1	0	0
123.0	0	1	0	1
136.0	0	1	0	1
139.0	0	1	0	1
145.0	0	1	0	1
165.0	0	0	0	1
166.0	0	1	0	0
176.0	0	1	0	1
179.0	0	0	0	1
181.0	0	1	0	0
194.0	0	0	0	1
195.0	0	1	0	0
214.0	0	1	0	1
220.0	0	0	0	1
221.0	0	1	0	0
235.0	0	1	0	1
293.0	0	0	0	1
295.0	0	1	0	0
336.0	0	0	0	1
337.0	0	1	0	0
379.0	0	0	0	1
381.0	0	1	0	0
460.0	0	0	0	1
463.0	0	1	0	0