## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2015-10-15/TR_Ank_Yes_1_2015-10-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2015-10-15/TR_Ank_Yes_1_2015-10-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/TR_Ank_Yes_1_2015-10-15/TR_Ank_Yes_1_2015-10-15.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: Fri Jan 20 09:06:44 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	9887053	34617900	0	0	3427831	2977454	0	0.118584	189532827

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	28631074	28631074
2.0	1.833061	2466740	2466740
3.0	2.527051	187675	187675
4.0	3.105188	14633	14633
5.0	3.58681	1709	1709
6.0	3.988031	529	529
7.0	4.322273	369	369
8.0	4.600716	295	295
9.0	4.832677	258	258
10.0	5.025914	217	217
11.0	5.186892	196	196
12.0	5.320997	164	164
13.0	5.432714	117	117
14.0	5.525782	165	165
15.0	5.603312	137	137
16.0	5.6679	115	115
17.0	5.721706	129	129
18.0	5.766529	85	85
19.0	5.80387	101	101
20.0	5.834977	73	73
21.0	5.860891	65	65
22.0	5.882479	62	62
23.0	5.900463	69	69
24.0	5.915445	53	53
25.0	5.927926	45	45
26.0	5.938323	56	56
27.0	5.946984	43	43
28.0	5.9542	58	58
29.0	5.960211	28	28
30.0	5.965218	38	38
31.0	5.96939	28	28
32.0	5.972865	29	29
33.0	5.97576	21	21
34.0	5.978172	25	25
35.0	5.980181	22	22
36.0	5.981855	22	22
37.0	5.983249	28	28
38.0	5.984411	21	21
39.0	5.985378	25	25
40.0	5.986185	16	16
41.0	5.986856	17	17
42.0	5.987416	24	24
43.0	5.987882	26	26
44.0	5.98827	18	18
45.0	5.988593	17	17
46.0	5.988863	9	9
47.0	5.989087	19	19
48.0	5.989274	13	13
49.0	5.98943	15	15
50.0	5.98956	16	16
51.0	5.989668	18	18
52.0	5.989758	16	16
53.0	5.989833	16	16
54.0	5.989895	10	10
55.0	5.989947	5	5
56.0	5.989991	12	12
57.0	5.990027	9	9
58.0	5.990057	17	17
59.0	5.990082	7	7
60.0	5.990103	7	7
61.0	5.99012	7	7
62.0	5.990135	6	6
63.0	5.990147	10	10
64.0	5.990157	5	5
65.0	5.990165	8	8
66.0	5.990172	8	8
67.0	5.990178	4	4
68.0	5.990183	7	7
69.0	5.990187	8	8
70.0	5.99019	4	4
71.0	5.990193	3	3
72.0	5.990196	4	4
73.0	5.990197	4	4
74.0	5.990199	3	3
75.0	5.9902	4	4
76.0	5.990202	3	3
77.0	5.990203	2	2
78.0	5.990203	5	5
79.0	5.990204	2	2
80.0	5.990204	7	7
81.0	5.990205	4	4
82.0	5.990205	5	5
83.0	5.990206	3	3
84.0	5.990206	1	1
85.0	5.990206	2	2
86.0	5.990206	3	3
87.0	5.990206	3	3
88.0	5.990207	2	2
89.0	5.990207	3	3
90.0	5.990207	3	3
91.0	5.990207	2	2
92.0	5.990207	3	3
93.0	5.990207	7	7
94.0	5.990207	3	3
95.0	5.990207	4	4
96.0	5.990207	2	2
97.0	5.990207	2	2
98.0	5.990207	2	2
99.0	5.990207	0	0
100.0	5.990207	2	2
101.0	0	3	3
102.0	0	1	1
103.0	0	3	3
104.0	0	2	2
105.0	0	2	2
106.0	0	4	4
107.0	0	1	1
109.0	0	1	1
110.0	0	2	2
111.0	0	2	2
112.0	0	1	1
113.0	0	2	2
114.0	0	3	3
115.0	0	1	1
120.0	0	3	3
121.0	0	1	1
122.0	0	3	3
123.0	0	1	1
125.0	0	1	1
127.0	0	2	2
130.0	0	1	1
131.0	0	1	1
133.0	0	2	2
134.0	0	1	1
135.0	0	1	1
136.0	0	1	1
137.0	0	1	1
139.0	0	1	1
143.0	0	2	2
144.0	0	1	1
147.0	0	1	1
148.0	0	2	2
151.0	0	1	1
154.0	0	2	2
155.0	0	1	1
157.0	0	2	2
158.0	0	1	1
159.0	0	1	1
164.0	0	1	1
173.0	0	1	1
184.0	0	1	1
208.0	0	1	1
217.0	0	1	1
221.0	0	1	1
224.0	0	1	1
233.0	0	1	1
267.0	0	1	1