## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/CA_Nov_Gas_0_2013-10-15/CA_Nov_Gas_0_2013-10-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/CA_Nov_Gas_0_2013-10-15/CA_Nov_Gas_0_2013-10-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/CA_Nov_Gas_0_2013-10-15/CA_Nov_Gas_0_2013-10-15.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: Thu May 25 23:10:18 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	3094051	76924277	0	0	1900785	1097379	0	0.026096	2670423270

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	74107883	74107883
2.0	1.971605	870793	870793
3.0	2.915621	52821	52821
4.0	3.832832	12804	12804
5.0	4.723998	4913	4913
6.0	5.58986	2524	2524
7.0	6.431135	1377	1377
8.0	7.248523	854	854
9.0	8.0427	577	577
10.0	8.814327	419	419
11.0	9.564043	297	297
12.0	10.292472	208	208
13.0	11.000216	159	159
14.0	11.687864	104	104
15.0	12.355986	111	111
16.0	13.005137	85	85
17.0	13.635855	45	45
18.0	14.248664	50	50
19.0	14.844071	47	47
20.0	15.422573	42	42
21.0	15.984648	39	39
22.0	16.530762	25	25
23.0	17.06137	23	23
24.0	17.576911	15	15
25.0	18.077813	25	25
26.0	18.564492	20	20
27.0	19.037351	11	11
28.0	19.496784	11	11
29.0	19.943171	15	15
30.0	20.376883	8	8
31.0	20.79828	12	12
32.0	21.207711	6	6
33.0	21.605516	10	10
34.0	21.992026	5	5
35.0	22.36756	11	11
36.0	22.732431	6	6
37.0	23.086942	7	7
38.0	23.431386	3	3
39.0	23.76605	7	7
40.0	24.091211	2	2
41.0	24.407139	2	2
42.0	24.714096	4	4
43.0	25.012337	4	4
44.0	25.30211	3	3
45.0	25.583654	0	0
46.0	25.857204	2	2
47.0	26.122987	2	2
48.0	26.381222	3	3
49.0	26.632125	4	4
50.0	26.875904	3	3
51.0	27.11276	1	1
52.0	27.342891	1	1
53.0	27.566487	4	4
54.0	27.783734	1	1
55.0	27.994813	5	5
56.0	28.199898	3	3
57.0	28.399159	2	2
58.0	28.592763	1	1
59.0	28.780869	4	4
60.0	28.963634	0	0
61.0	29.141209	0	0
62.0	29.313742	1	1
63.0	29.481375	2	2
64.0	29.644249	0	0
65.0	29.802498	1	1
66.0	29.956254	1	1
67.0	30.105643	2	2
68.0	30.250791	0	0
69.0	30.391817	0	0
70.0	30.528839	0	0
71.0	30.66197	0	0
72.0	30.791321	3	3
73.0	30.916998	0	0
74.0	31.039108	0	0
75.0	31.157749	1	1
76.0	31.273023	1	1
77.0	31.385022	1	1
78.0	31.493842	0	0
79.0	31.599572	0	0
80.0	31.702299	2	2
81.0	31.80211	1	1
82.0	31.899086	1	1
83.0	31.993309	0	0
84.0	32.084856	0	0
85.0	32.173804	0	0
86.0	32.260226	1	1
87.0	32.344194	1	1
88.0	32.425778	1	1
89.0	32.505045	1	1
90.0	32.582061	0	0
91.0	32.656891	3	3
92.0	32.729596	0	0
93.0	32.800236	1	1
94.0	32.868871	0	0
95.0	32.935556	1	1
96.0	33.000348	0	0
97.0	33.0633	0	0
98.0	33.124465	0	0
99.0	33.183893	0	0
100.0	33.241634	0	0
105.0	0	2	2
106.0	0	1	1
123.0	0	2	2
142.0	0	1	1
172.0	0	1	1
181.0	0	1	1
184.0	0	1	1
193.0	0	1	1
196.0	0	1	1
235.0	0	1	1