## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Pol_Pyr_1_2015-08-26/UA_Pol_Pyr_1_2015-08-26.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Pol_Pyr_1_2015-08-26/UA_Pol_Pyr_1_2015-08-26.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Pol_Pyr_1_2015-08-26/UA_Pol_Pyr_1_2015-08-26.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 17:37:25 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	8299351	28626605	0	0	3068698	4101776	0	0.171957	90104267

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	20675044	20675044
2.0	1.727817	3012277	3012277
3.0	2.257535	399816	399816
4.0	2.643073	51260	51260
5.0	2.923674	6893	6893
6.0	3.1279	1234	1234
7.0	3.27654	461	461
8.0	3.384722	281	281
9.0	3.463459	238	238
10.0	3.520765	207	207
11.0	3.562474	173	173
12.0	3.59283	144	144
13.0	3.614923	116	116
14.0	3.631003	119	119
15.0	3.642707	122	122
16.0	3.651225	95	95
17.0	3.657424	91	91
18.0	3.661936	96	96
19.0	3.66522	73	73
20.0	3.667611	75	75
21.0	3.66935	78	78
22.0	3.670616	71	71
23.0	3.671538	73	73
24.0	3.672208	74	74
25.0	3.672697	57	57
26.0	3.673052	49	49
27.0	3.67331	43	43
28.0	3.673499	51	51
29.0	3.673636	50	50
30.0	3.673735	36	36
31.0	3.673808	45	45
32.0	3.673861	41	41
33.0	3.673899	42	42
34.0	3.673927	33	33
35.0	3.673947	33	33
36.0	3.673962	39	39
37.0	3.673973	27	27
38.0	3.673981	24	24
39.0	3.673987	30	30
40.0	3.673991	16	16
41.0	3.673994	23	23
42.0	3.673996	25	25
43.0	3.673998	18	18
44.0	3.673999	13	13
45.0	3.674	12	12
46.0	3.674	19	19
47.0	3.674001	23	23
48.0	3.674001	22	22
49.0	3.674001	13	13
50.0	3.674001	20	20
51.0	3.674002	21	21
52.0	3.674002	12	12
53.0	3.674002	13	13
54.0	3.674002	13	13
55.0	3.674002	21	21
56.0	3.674002	8	8
57.0	3.674002	11	11
58.0	3.674002	10	10
59.0	3.674002	10	10
60.0	3.674002	17	17
61.0	3.674002	21	21
62.0	3.674002	18	18
63.0	3.674002	9	9
64.0	3.674002	6	6
65.0	3.674002	14	14
66.0	3.674002	10	10
67.0	3.674002	7	7
68.0	3.674002	7	7
69.0	3.674002	11	11
70.0	3.674002	14	14
71.0	3.674002	7	7
72.0	3.674002	4	4
73.0	3.674002	3	3
74.0	3.674002	9	9
75.0	3.674002	1	1
76.0	3.674002	4	4
77.0	3.674002	7	7
78.0	3.674002	4	4
79.0	3.674002	9	9
80.0	3.674002	2	2
81.0	3.674002	3	3
82.0	3.674002	8	8
83.0	3.674002	2	2
84.0	3.674002	4	4
85.0	3.674002	2	2
86.0	3.674002	3	3
87.0	3.674002	5	5
88.0	3.674002	5	5
89.0	3.674002	10	10
90.0	3.674002	1	1
91.0	3.674002	4	4
92.0	3.674002	6	6
93.0	3.674002	3	3
94.0	3.674002	3	3
95.0	3.674002	2	2
96.0	3.674002	2	2
97.0	3.674002	5	5
98.0	3.674002	8	8
99.0	3.674002	1	1
100.0	3.674002	2	2
101.0	0	4	4
102.0	0	2	2
103.0	0	5	5
104.0	0	3	3
106.0	0	8	8
107.0	0	1	1
108.0	0	3	3
109.0	0	4	4
110.0	0	1	1
111.0	0	2	2
113.0	0	3	3
114.0	0	2	2
115.0	0	1	1
116.0	0	2	2
118.0	0	2	2
119.0	0	5	5
120.0	0	2	2
121.0	0	1	1
122.0	0	1	1
123.0	0	4	4
125.0	0	2	2
126.0	0	1	1
128.0	0	3	3
129.0	0	1	1
130.0	0	1	1
131.0	0	1	1
132.0	0	4	4
133.0	0	4	4
134.0	0	1	1
135.0	0	1	1
136.0	0	1	1
137.0	0	2	2
138.0	0	3	3
139.0	0	1	1
140.0	0	1	1
141.0	0	2	2
143.0	0	2	2
144.0	0	1	1
147.0	0	1	1
148.0	0	2	2
152.0	0	1	1
153.0	0	2	2
154.0	0	2	2
157.0	0	1	1
158.0	0	2	2
159.0	0	5	5
162.0	0	1	1
163.0	0	1	1
164.0	0	1	1
167.0	0	1	1
169.0	0	1	1
170.0	0	2	2
178.0	0	1	1
179.0	0	1	1
180.0	0	1	1
181.0	0	1	1
182.0	0	2	2
185.0	0	1	1
187.0	0	2	2
188.0	0	1	1
189.0	0	1	1
193.0	0	1	1
194.0	0	1	1
203.0	0	1	1
204.0	0	1	1
211.0	0	3	3
212.0	0	1	1
216.0	0	1	1
220.0	0	1	1
221.0	0	1	1
229.0	0	1	1
234.0	0	1	1
260.0	0	1	1
294.0	0	1	1
298.0	0	1	1