## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Uma_1_2015-09-26/UA_Che_Uma_1_2015-09-26.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Uma_1_2015-09-26/UA_Che_Uma_1_2015-09-26.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Uma_1_2015-09-26/UA_Che_Uma_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 08:48:35 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	8488810	30124244	0	0	2767619	2424566	0	0.11081	176958499

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	25182734	25182734
2.0	1.843468	2054322	2054322
3.0	2.554906	141649	141649
4.0	3.154981	10195	10195
5.0	3.661126	1424	1424
6.0	4.088042	600	600
7.0	4.448132	409	409
8.0	4.751857	263	263
9.0	5.008039	223	223
10.0	5.22412	183	183
11.0	5.406378	175	175
12.0	5.560107	137	137
13.0	5.689772	104	104
14.0	5.79914	105	105
15.0	5.891389	84	84
16.0	5.969198	88	88
17.0	6.034827	70	70
18.0	6.090183	67	67
19.0	6.136874	40	40
20.0	6.176257	48	48
21.0	6.209474	36	36
22.0	6.237493	39	39
23.0	6.261125	38	38
24.0	6.281058	37	37
25.0	6.297871	29	29
26.0	6.312053	24	24
27.0	6.324014	21	21
28.0	6.334103	19	19
29.0	6.342613	27	27
30.0	6.349791	21	21
31.0	6.355845	24	24
32.0	6.360951	19	19
33.0	6.365259	20	20
34.0	6.368892	16	16
35.0	6.371956	11	11
36.0	6.37454	16	16
37.0	6.376721	12	12
38.0	6.378559	12	12
39.0	6.38011	9	9
40.0	6.381419	16	16
41.0	6.382522	14	14
42.0	6.383453	8	8
43.0	6.384238	7	7
44.0	6.3849	6	6
45.0	6.385458	8	8
46.0	6.385929	10	10
47.0	6.386327	2	2
48.0	6.386662	11	11
49.0	6.386945	5	5
50.0	6.387183	3	3
51.0	6.387384	7	7
52.0	6.387554	10	10
53.0	6.387697	9	9
54.0	6.387817	2	2
55.0	6.387919	1	1
56.0	6.388005	7	7
57.0	6.388078	3	3
58.0	6.388139	1	1
59.0	6.38819	4	4
60.0	6.388234	3	3
61.0	6.38827	3	3
62.0	6.388301	4	4
63.0	6.388327	3	3
64.0	6.388349	3	3
65.0	6.388368	3	3
66.0	6.388383	7	7
67.0	6.388397	5	5
68.0	6.388408	1	1
69.0	6.388417	4	4
70.0	6.388425	5	5
71.0	6.388432	4	4
72.0	6.388437	1	1
73.0	6.388442	0	0
74.0	6.388446	4	4
75.0	6.38845	2	2
76.0	6.388452	1	1
77.0	6.388455	3	3
78.0	6.388457	1	1
79.0	6.388459	1	1
80.0	6.38846	0	0
81.0	6.388461	2	2
82.0	6.388462	0	0
83.0	6.388463	2	2
84.0	6.388464	1	1
85.0	6.388464	1	1
86.0	6.388465	1	1
87.0	6.388465	0	0
88.0	6.388466	1	1
89.0	6.388466	2	2
90.0	6.388466	2	2
91.0	6.388467	0	0
92.0	6.388467	2	2
93.0	6.388467	0	0
94.0	6.388467	2	2
95.0	6.388467	0	0
96.0	6.388467	0	0
97.0	6.388467	1	1
98.0	6.388467	0	0
99.0	6.388467	1	1
100.0	6.388467	0	0
108.0	0	1	1
110.0	0	1	1
113.0	0	1	1
115.0	0	1	1
116.0	0	2	2
117.0	0	1	1
120.0	0	1	1
121.0	0	1	1
122.0	0	1	1
123.0	0	1	1
127.0	0	1	1
131.0	0	2	2
137.0	0	1	1
142.0	0	1	1
143.0	0	1	1
144.0	0	1	1
146.0	0	1	1
160.0	0	3	3
167.0	0	2	2
178.0	0	1	1
186.0	0	1	1
196.0	0	1	1
319.0	0	1	1
404.0	0	1	1