## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Wie_Gro_1_2012-08-03/AT_Wie_Gro_1_2012-08-03.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Wie_Gro_1_2012-08-03/AT_Wie_Gro_1_2012-08-03.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/AT_Wie_Gro_1_2012-08-03/AT_Wie_Gro_1_2012-08-03.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 07:38:32 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	1213918	20955895	0	0	220409	213269	0	0.015001	1022569990

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	20492319	20492319
2.0	1.979715	54069	54069
3.0	2.939557	4115	4115
4.0	3.879929	876	876
5.0	4.801225	337	337
6.0	5.703833	200	200
7.0	6.588132	121	121
8.0	7.454493	96	96
9.0	8.30328	100	100
10.0	9.13485	83	83
11.0	9.949551	56	56
12.0	10.747727	58	58
13.0	11.529711	37	37
14.0	12.295833	31	31
15.0	13.046415	24	24
16.0	13.781771	26	26
17.0	14.502211	18	18
18.0	15.208036	19	19
19.0	15.899544	21	21
20.0	16.577025	11	11
21.0	17.240764	11	11
22.0	17.891038	7	7
23.0	18.528122	7	7
24.0	19.152283	7	7
25.0	19.763783	5	5
26.0	20.362878	6	6
27.0	20.949821	9	9
28.0	21.524859	6	6
29.0	22.088231	9	9
30.0	22.640176	1	1
31.0	23.180924	6	6
32.0	23.710704	5	5
33.0	24.229737	4	4
34.0	24.738242	6	6
35.0	25.236432	3	3
36.0	25.724516	3	3
37.0	26.202699	6	6
38.0	26.671183	4	4
39.0	27.130163	2	2
40.0	27.579833	2	2
41.0	28.020382	4	4
42.0	28.451994	4	4
43.0	28.874851	3	3
44.0	29.289131	2	2
45.0	29.695006	3	3
46.0	30.092649	7	7
47.0	30.482226	4	4
48.0	30.8639	3	3
49.0	31.237832	2	2
50.0	31.604179	0	0
51.0	31.963095	3	3
52.0	32.31473	2	2
53.0	32.659232	1	1
54.0	32.996746	2	2
55.0	33.327414	3	3
56.0	33.651374	2	2
57.0	33.968762	1	1
58.0	34.279713	3	3
59.0	34.584356	1	1
60.0	34.882819	1	1
61.0	35.175228	1	1
62.0	35.461706	1	1
63.0	35.742372	1	1
64.0	36.017345	0	0
65.0	36.286741	1	1
66.0	36.550672	0	0
67.0	36.809249	1	1
68.0	37.06258	2	2
69.0	37.310773	4	4
70.0	37.553932	2	2
71.0	37.792158	1	1
72.0	38.025552	3	3
73.0	38.254211	2	2
74.0	38.478232	2	2
75.0	38.697709	0	0
76.0	38.912734	2	2
77.0	39.123397	1	1
78.0	39.329787	0	0
79.0	39.53199	1	1
80.0	39.730091	3	3
81.0	39.924174	2	2
82.0	40.114321	3	3
83.0	40.30061	0	0
84.0	40.48312	1	1
85.0	40.661928	2	2
86.0	40.837109	0	0
87.0	41.008737	3	3
88.0	41.176883	1	1
89.0	41.341618	1	1
90.0	41.503011	0	0
91.0	41.661131	3	3
92.0	41.816044	0	0
93.0	41.967814	0	0
94.0	42.116505	0	0
95.0	42.26218	0	0
96.0	42.4049	1	1
97.0	42.544725	2	2
98.0	42.681714	1	1
99.0	42.815924	2	2
100.0	42.947412	1	1
101.0	0	1	1
103.0	0	1	1
106.0	0	1	1
107.0	0	1	1
109.0	0	1	1
110.0	0	2	2
111.0	0	2	2
112.0	0	1	1
113.0	0	1	1
115.0	0	1	1
116.0	0	1	1
118.0	0	1	1
120.0	0	3	3
122.0	0	2	2
126.0	0	1	1
132.0	0	1	1
135.0	0	1	1
137.0	0	2	2
138.0	0	1	1
140.0	0	2	2
141.0	0	2	2
148.0	0	1	1
153.0	0	1	1
159.0	0	1	1
160.0	0	2	2
161.0	0	2	2
162.0	0	1	1
163.0	0	1	1
167.0	0	1	1
168.0	0	1	1
170.0	0	1	1
171.0	0	2	2
176.0	0	1	1
177.0	0	1	1
180.0	0	1	1
181.0	0	1	1
184.0	0	2	2
187.0	0	2	2
188.0	0	1	1
198.0	0	1	1
202.0	0	1	1
203.0	0	1	1
210.0	0	1	1
211.0	0	1	1
212.0	0	1	1
214.0	0	2	2
224.0	0	2	2
228.0	0	1	1
231.0	0	1	1
232.0	0	2	2
250.0	0	1	1
253.0	0	2	2
255.0	0	1	1
269.0	0	1	1
270.0	0	1	1
272.0	0	1	1
282.0	0	1	1
290.0	0	1	1
319.0	0	1	1
340.0	0	1	1
343.0	0	1	1
358.0	0	1	1
404.0	0	1	1
412.0	0	1	1
442.0	0	1	1
590.0	0	1	1
591.0	0	1	1
629.0	0	1	1
698.0	0	1	1
759.0	0	1	1
817.0	0	1	1
935.0	0	1	1
1068.0	0	1	1
1155.0	0	1	1
1163.0	0	1	1
1201.0	0	1	1
1357.0	0	1	1
1392.0	0	1	1
1690.0	0	1	1
1844.0	0	1	1
2132.0	0	1	1
2175.0	0	1	1
2206.0	0	1	1
2826.0	0	1	1
3235.0	0	1	1
4152.0	0	1	1
4198.0	0	1	1
8811.0	0	1	1
11638.0	0	1	1
12404.0	0	1	1
13570.0	0	1	1
31023.0	0	1	1