## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output/GR_Kri_Ira_1_2017-11-06/GR_Kri_Ira_1_2017-11-06.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/GR_Kri_Ira_1_2017-11-06/GR_Kri_Ira_1_2017-11-06.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/GR_Kri_Ira_1_2017-11-06/GR_Kri_Ira_1_2017-11-06.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 08:50:40 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	2755814	26644478	0	0	1539152	9920897	202017	0.381498	26475633

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	optical_sets	non_optical_sets
1.0	1.004433	9649395	0	9721286
2.0	1.371594	3870151	197428	3860577
3.0	1.505806	1477578	2245	1451618
4.0	1.554866	540349	28	521462
5.0	1.5728	191147	1	181498
6.0	1.579355	67684	1	63219
7.0	1.581751	24687	1	22688
8.0	1.582627	9145	0	8316
9.0	1.582947	3705	0	3436
10.0	1.583064	1971	0	1829
11.0	1.583107	1085	0	1047
12.0	1.583123	708	0	693
13.0	1.583129	530	0	506
14.0	1.583131	412	0	401
15.0	1.583131	314	0	306
16.0	1.583132	247	0	245
17.0	1.583132	222	0	220
18.0	1.583132	171	0	171
19.0	1.583132	147	0	140
20.0	1.583132	129	0	131
21.0	1.583132	119	0	119
22.0	1.583132	104	0	102
23.0	1.583132	86	0	85
24.0	1.583132	89	0	89
25.0	1.583132	70	0	69
26.0	1.583132	49	0	44
27.0	1.583132	44	0	50
28.0	1.583132	69	0	68
29.0	1.583132	57	0	56
30.0	1.583132	38	0	37
31.0	1.583132	40	0	38
32.0	1.583132	32	0	31
33.0	1.583132	38	0	40
34.0	1.583132	27	0	29
35.0	1.583132	32	0	31
36.0	1.583132	31	0	29
37.0	1.583132	33	0	29
38.0	1.583132	16	0	18
39.0	1.583132	20	0	19
40.0	1.583132	17	0	17
41.0	1.583132	11	0	14
42.0	1.583132	16	0	18
43.0	1.583132	21	0	18
44.0	1.583132	12	0	12
45.0	1.583132	14	0	13
46.0	1.583132	9	0	9
47.0	1.583132	19	0	21
48.0	1.583132	13	0	11
49.0	1.583132	10	0	9
50.0	1.583132	12	0	13
51.0	1.583132	7	0	5
52.0	1.583132	8	0	8
53.0	1.583132	4	0	4
54.0	1.583132	5	0	6
55.0	1.583132	9	0	8
56.0	1.583132	8	0	9
57.0	1.583132	3	0	4
58.0	1.583132	8	0	7
59.0	1.583132	7	0	7
60.0	1.583132	4	0	4
61.0	1.583132	4	0	6
62.0	1.583132	6	0	4
63.0	1.583132	6	0	5
64.0	1.583132	3	0	4
65.0	1.583132	7	0	6
66.0	1.583132	2	0	3
67.0	1.583132	11	0	10
68.0	1.583132	4	0	4
69.0	1.583132	4	0	6
70.0	1.583132	4	0	3
71.0	1.583132	2	0	2
72.0	1.583132	5	0	5
73.0	1.583132	3	0	3
74.0	1.583132	5	0	5
75.0	1.583132	8	0	8
76.0	1.583132	4	0	4
77.0	1.583132	4	0	3
78.0	1.583132	3	0	4
79.0	1.583132	3	0	3
80.0	1.583132	1	0	0
81.0	1.583132	1	0	1
82.0	1.583132	1	0	1
83.0	1.583132	1	0	2
84.0	1.583132	3	0	2
85.0	1.583132	0	0	2
86.0	1.583132	1	0	1
87.0	1.583132	2	0	2
88.0	1.583132	2	0	1
89.0	1.583132	2	0	1
90.0	1.583132	2	0	2
91.0	1.583132	2	0	2
92.0	1.583132	1	0	2
93.0	1.583132	1	0	1
94.0	1.583132	2	0	1
95.0	1.583132	2	0	2
96.0	1.583132	0	0	0
97.0	1.583132	2	0	3
98.0	1.583132	0	0	0
99.0	1.583132	1	0	1
100.0	1.583132	0	0	1
101.0	0	2	0	2
102.0	0	6	0	4
103.0	0	4	0	6
104.0	0	3	0	2
105.0	0	2	0	1
106.0	0	1	0	1
107.0	0	1	0	1
108.0	0	2	0	3
109.0	0	1	0	0
110.0	0	1	0	1
111.0	0	1	0	1
112.0	0	1	0	2
113.0	0	2	0	1
115.0	0	1	0	2
116.0	0	1	0	0
118.0	0	1	0	1
121.0	0	4	0	4
122.0	0	2	0	2
123.0	0	1	0	1
125.0	0	0	0	1
126.0	0	1	0	0
127.0	0	1	0	1
129.0	0	0	0	2
130.0	0	1	0	2
131.0	0	2	0	1
132.0	0	2	0	1
133.0	0	1	0	0
135.0	0	2	0	2
136.0	0	0	0	1
137.0	0	2	0	1
141.0	0	1	0	1
143.0	0	1	0	1
145.0	0	0	0	1
147.0	0	1	0	1
148.0	0	1	0	0
150.0	0	2	0	2
152.0	0	1	0	1
155.0	0	1	0	1
156.0	0	1	0	1
158.0	0	0	0	1
159.0	0	1	0	0
166.0	0	1	0	1
168.0	0	1	0	1
173.0	0	1	0	1
181.0	0	0	0	1
183.0	0	1	0	0
184.0	0	0	0	1
185.0	0	1	0	0
187.0	0	0	0	1
188.0	0	1	0	0
193.0	0	0	0	1
194.0	0	1	0	0
195.0	0	1	0	1
196.0	0	1	0	1
200.0	0	0	0	1
202.0	0	1	0	2
203.0	0	1	0	0
204.0	0	2	0	1
205.0	0	0	0	1
206.0	0	1	0	0
215.0	0	1	0	1
222.0	0	0	0	1
223.0	0	1	0	0
227.0	0	1	0	1
232.0	0	1	0	1
244.0	0	2	0	2
248.0	0	0	0	1
249.0	0	1	0	0
253.0	0	1	0	1
266.0	0	1	0	1
343.0	0	0	0	1
345.0	0	1	0	0
352.0	0	0	0	1
353.0	0	1	0	0
360.0	0	1	0	1
390.0	0	1	0	1
442.0	0	0	0	1
444.0	0	1	0	0
456.0	0	0	0	1
457.0	0	1	0	0
471.0	0	0	0	1
473.0	0	1	0	0
615.0	0	0	0	1
620.0	0	1	0	0
702.0	0	1	0	1
1312.0	0	0	0	1
1318.0	0	1	0	0