## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2015-06-30/UA_Ode_Ode_1_2015-06-30.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2015-06-30/UA_Ode_Ode_1_2015-06-30.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Ode_Ode_1_2015-06-30/UA_Ode_Ode_1_2015-06-30.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 17:23:36 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	7335564	31216937	0	0	2527465	3938995	0	0.149141	113058131

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	23552561	23552561
2.0	1.758726	3026457	3026457
3.0	2.334392	351685	351685
4.0	2.771165	39701	39701
5.0	3.102556	4842	4842
6.0	3.353991	940	940
7.0	3.544762	404	404
8.0	3.689504	271	271
9.0	3.799324	256	256
10.0	3.882648	205	205
11.0	3.945867	188	188
12.0	3.993834	151	151
13.0	4.030227	144	144
14.0	4.05784	137	137
15.0	4.07879	130	130
16.0	4.094686	94	94
17.0	4.106746	87	87
18.0	4.115897	88	88
19.0	4.12284	66	66
20.0	4.128107	83	83
21.0	4.132104	51	51
22.0	4.135136	61	61
23.0	4.137437	55	55
24.0	4.139183	50	50
25.0	4.140507	39	39
26.0	4.141512	40	40
27.0	4.142275	28	28
28.0	4.142853	33	33
29.0	4.143292	30	30
30.0	4.143625	21	21
31.0	4.143878	31	31
32.0	4.144069	24	24
33.0	4.144215	31	31
34.0	4.144325	20	20
35.0	4.144409	27	27
36.0	4.144473	29	29
37.0	4.144521	21	21
38.0	4.144557	12	12
39.0	4.144585	16	16
40.0	4.144606	21	21
41.0	4.144622	30	30
42.0	4.144634	20	20
43.0	4.144643	16	16
44.0	4.14465	8	8
45.0	4.144656	12	12
46.0	4.14466	13	13
47.0	4.144663	16	16
48.0	4.144665	12	12
49.0	4.144667	11	11
50.0	4.144668	12	12
51.0	4.144669	14	14
52.0	4.14467	5	5
53.0	4.14467	6	6
54.0	4.144671	12	12
55.0	4.144671	13	13
56.0	4.144672	7	7
57.0	4.144672	3	3
58.0	4.144672	9	9
59.0	4.144672	7	7
60.0	4.144672	4	4
61.0	4.144672	2	2
62.0	4.144672	2	2
63.0	4.144672	6	6
64.0	4.144672	8	8
65.0	4.144672	9	9
66.0	4.144672	8	8
67.0	4.144672	4	4
68.0	4.144672	2	2
69.0	4.144672	3	3
70.0	4.144672	3	3
71.0	4.144672	3	3
72.0	4.144672	4	4
73.0	4.144672	3	3
74.0	4.144672	3	3
75.0	4.144672	3	3
76.0	4.144672	1	1
77.0	4.144672	0	0
78.0	4.144672	2	2
79.0	4.144672	6	6
80.0	4.144672	2	2
81.0	4.144672	2	2
82.0	4.144672	4	4
83.0	4.144672	4	4
84.0	4.144672	3	3
85.0	4.144672	7	7
86.0	4.144672	0	0
87.0	4.144672	1	1
88.0	4.144672	2	2
89.0	4.144672	3	3
90.0	4.144672	1	1
91.0	4.144672	2	2
92.0	4.144672	3	3
93.0	4.144672	0	0
94.0	4.144672	0	0
95.0	4.144672	0	0
96.0	4.144672	1	1
97.0	4.144672	3	3
98.0	4.144672	0	0
99.0	4.144672	0	0
100.0	4.144672	0	0
102.0	0	1	1
103.0	0	1	1
104.0	0	2	2
105.0	0	1	1
106.0	0	1	1
107.0	0	1	1
109.0	0	1	1
110.0	0	1	1
111.0	0	1	1
112.0	0	1	1
113.0	0	2	2
117.0	0	1	1
119.0	0	1	1
121.0	0	1	1
122.0	0	1	1
123.0	0	1	1
125.0	0	1	1
127.0	0	2	2
129.0	0	2	2
130.0	0	1	1
134.0	0	1	1
135.0	0	1	1
136.0	0	1	1
137.0	0	1	1
138.0	0	1	1
143.0	0	1	1
145.0	0	1	1
147.0	0	1	1
151.0	0	1	1
154.0	0	1	1
160.0	0	1	1
170.0	0	1	1
171.0	0	1	1
174.0	0	1	1
177.0	0	1	1
294.0	0	1	1