## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2015-09-26/UA_Ode_Ode_1_2015-09-26.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2015-09-26/UA_Ode_Ode_1_2015-09-26.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2015-09-26/UA_Ode_Ode_1_2015-09-26.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 17:38:38 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	10145694	26453995	0	0	2593485	2078433	0	0.107057	159412739

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	22070189	22070189
2.0	1.847092	1749645	1749645
3.0	2.564656	122818	122818
4.0	3.172498	9586	9586
5.0	3.687396	1489	1489
6.0	4.123562	662	662
7.0	4.493034	454	454
8.0	4.806011	342	342
9.0	5.071131	221	221
10.0	5.295712	203	203
11.0	5.485953	148	148
12.0	5.647104	131	131
13.0	5.783614	109	109
14.0	5.89925	108	108
15.0	5.997205	79	79
16.0	6.080181	71	71
17.0	6.15047	72	72
18.0	6.210011	59	59
19.0	6.260447	51	51
20.0	6.303172	47	47
21.0	6.339363	38	38
22.0	6.370021	42	42
23.0	6.39599	28	28
24.0	6.417989	36	36
25.0	6.436624	17	17
26.0	6.45241	19	19
27.0	6.465781	28	28
28.0	6.477108	16	16
29.0	6.486704	14	14
30.0	6.494831	22	22
31.0	6.501717	17	17
32.0	6.507549	13	13
33.0	6.512489	8	8
34.0	6.516674	19	19
35.0	6.52022	12	12
36.0	6.523223	10	10
37.0	6.525766	9	9
38.0	6.527921	12	12
39.0	6.529747	10	10
40.0	6.531293	10	10
41.0	6.532603	12	12
42.0	6.533712	8	8
43.0	6.534652	8	8
44.0	6.535448	4	4
45.0	6.536123	8	8
46.0	6.536694	8	8
47.0	6.537178	8	8
48.0	6.537588	6	6
49.0	6.537935	6	6
50.0	6.538229	5	5
51.0	6.538479	4	4
52.0	6.53869	5	5
53.0	6.538868	5	5
54.0	6.53902	3	3
55.0	6.539148	4	4
56.0	6.539257	5	5
57.0	6.539349	1	1
58.0	6.539427	5	5
59.0	6.539493	2	2
60.0	6.539549	6	6
61.0	6.539596	5	5
62.0	6.539637	5	5
63.0	6.539671	3	3
64.0	6.539699	5	5
65.0	6.539724	2	2
66.0	6.539744	3	3
67.0	6.539762	2	2
68.0	6.539777	0	0
69.0	6.539789	2	2
70.0	6.5398	2	2
71.0	6.539809	3	3
72.0	6.539817	2	2
73.0	6.539823	5	5
74.0	6.539829	1	1
75.0	6.539833	2	2
76.0	6.539837	4	4
77.0	6.539841	1	1
78.0	6.539843	0	0
79.0	6.539846	3	3
80.0	6.539848	1	1
81.0	6.53985	1	1
82.0	6.539851	0	0
83.0	6.539852	0	0
84.0	6.539853	2	2
85.0	6.539854	2	2
86.0	6.539855	0	0
87.0	6.539856	1	1
88.0	6.539856	2	2
89.0	6.539856	1	1
90.0	6.539857	0	0
91.0	6.539857	1	1
92.0	6.539857	0	0
93.0	6.539858	0	0
94.0	6.539858	3	3
95.0	6.539858	0	0
96.0	6.539858	0	0
97.0	6.539858	1	1
98.0	6.539858	1	1
99.0	6.539859	2	2
100.0	6.539859	0	0
102.0	0	2	2
103.0	0	2	2
104.0	0	2	2
112.0	0	1	1
114.0	0	1	1
115.0	0	1	1
117.0	0	1	1
121.0	0	1	1
123.0	0	1	1
124.0	0	1	1
129.0	0	1	1
142.0	0	1	1
156.0	0	2	2
157.0	0	1	1
158.0	0	1	1
170.0	0	1	1
176.0	0	1	1
178.0	0	1	1
199.0	0	1	1
212.0	0	1	1
220.0	0	1	1
261.0	0	1	1
299.0	0	1	1