## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2015-10-15/US_Pen_Lin_1_2015-10-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2015-10-15/US_Pen_Lin_1_2015-10-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Pen_Lin_1_2015-10-15/US_Pen_Lin_1_2015-10-15.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: Fri Jan 20 20:19:31 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	740026	51574616	0	0	321374	5627032	0	0.111421	218830038

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	40082967	40082967
2.0	1.790031	4325084	4325084
3.0	2.414179	463218	463218
4.0	2.907276	55392	55392
5.0	3.296837	9228	9228
6.0	3.604603	2581	2581
7.0	3.847747	1264	1264
8.0	4.039838	797	797
9.0	4.191596	548	548
10.0	4.31149	428	428
11.0	4.40621	341	341
12.0	4.481041	278	278
13.0	4.54016	263	263
14.0	4.586866	208	208
15.0	4.623765	214	214
16.0	4.652916	133	133
17.0	4.675947	145	145
18.0	4.694142	134	134
19.0	4.708516	102	102
20.0	4.719873	87	87
21.0	4.728844	87	87
22.0	4.735932	90	90
23.0	4.741532	76	76
24.0	4.745956	59	59
25.0	4.749451	58	58
26.0	4.752212	53	53
27.0	4.754394	42	42
28.0	4.756117	58	58
29.0	4.757479	47	47
30.0	4.758554	38	38
31.0	4.759404	55	55
32.0	4.760076	30	30
33.0	4.760606	39	39
34.0	4.761025	30	30
35.0	4.761356	30	30
36.0	4.761618	32	32
37.0	4.761824	21	21
38.0	4.761987	23	23
39.0	4.762116	30	30
40.0	4.762218	18	18
41.0	4.762299	32	32
42.0	4.762362	21	21
43.0	4.762413	24	24
44.0	4.762452	19	19
45.0	4.762484	13	13
46.0	4.762508	22	22
47.0	4.762528	18	18
48.0	4.762543	13	13
49.0	4.762556	14	14
50.0	4.762565	19	19
51.0	4.762573	10	10
52.0	4.762579	16	16
53.0	4.762584	12	12
54.0	4.762587	16	16
55.0	4.76259	7	7
56.0	4.762593	15	15
57.0	4.762595	14	14
58.0	4.762596	9	9
59.0	4.762597	6	6
60.0	4.762598	12	12
61.0	4.762599	8	8
62.0	4.762599	6	6
63.0	4.7626	7	7
64.0	4.7626	9	9
65.0	4.762601	7	7
66.0	4.762601	11	11
67.0	4.762601	2	2
68.0	4.762601	7	7
69.0	4.762601	7	7
70.0	4.762601	6	6
71.0	4.762601	6	6
72.0	4.762601	9	9
73.0	4.762601	8	8
74.0	4.762601	7	7
75.0	4.762602	6	6
76.0	4.762602	3	3
77.0	4.762602	4	4
78.0	4.762602	4	4
79.0	4.762602	7	7
80.0	4.762602	4	4
81.0	4.762602	3	3
82.0	4.762602	7	7
83.0	4.762602	5	5
84.0	4.762602	5	5
85.0	4.762602	3	3
86.0	4.762602	2	2
87.0	4.762602	5	5
88.0	4.762602	4	4
89.0	4.762602	5	5
90.0	4.762602	3	3
91.0	4.762602	4	4
92.0	4.762602	6	6
93.0	4.762602	3	3
94.0	4.762602	1	1
95.0	4.762602	3	3
96.0	4.762602	4	4
97.0	4.762602	2	2
98.0	4.762602	4	4
99.0	4.762602	2	2
100.0	4.762602	5	5
101.0	0	8	8
102.0	0	4	4
103.0	0	3	3
104.0	0	2	2
105.0	0	2	2
107.0	0	1	1
108.0	0	1	1
109.0	0	3	3
110.0	0	2	2
111.0	0	5	5
112.0	0	4	4
113.0	0	3	3
114.0	0	4	4
115.0	0	2	2
116.0	0	1	1
118.0	0	1	1
119.0	0	1	1
120.0	0	3	3
121.0	0	5	5
122.0	0	3	3
123.0	0	2	2
124.0	0	2	2
125.0	0	2	2
127.0	0	1	1
128.0	0	1	1
129.0	0	1	1
130.0	0	1	1
131.0	0	1	1
133.0	0	4	4
134.0	0	1	1
135.0	0	2	2
136.0	0	1	1
138.0	0	1	1
139.0	0	1	1
140.0	0	2	2
141.0	0	2	2
142.0	0	1	1
143.0	0	1	1
144.0	0	1	1
147.0	0	2	2
148.0	0	1	1
149.0	0	1	1
150.0	0	3	3
151.0	0	2	2
152.0	0	2	2
153.0	0	2	2
155.0	0	2	2
156.0	0	4	4
157.0	0	1	1
158.0	0	3	3
159.0	0	2	2
160.0	0	1	1
161.0	0	2	2
162.0	0	2	2
164.0	0	2	2
165.0	0	2	2
166.0	0	3	3
167.0	0	3	3
168.0	0	2	2
170.0	0	1	1
172.0	0	1	1
173.0	0	1	1
174.0	0	2	2
176.0	0	2	2
177.0	0	1	1
178.0	0	1	1
179.0	0	2	2
180.0	0	1	1
181.0	0	1	1
184.0	0	1	1
187.0	0	1	1
188.0	0	3	3
189.0	0	1	1
193.0	0	1	1
196.0	0	2	2
198.0	0	1	1
199.0	0	1	1
200.0	0	1	1
202.0	0	4	4
203.0	0	1	1
204.0	0	1	1
207.0	0	1	1
216.0	0	1	1
218.0	0	1	1
219.0	0	1	1
223.0	0	1	1
224.0	0	2	2
226.0	0	4	4
232.0	0	1	1
233.0	0	3	3
235.0	0	1	1
240.0	0	1	1
244.0	0	1	1
253.0	0	2	2
262.0	0	1	1
263.0	0	1	1
264.0	0	1	1
266.0	0	1	1
268.0	0	1	1
269.0	0	1	1
272.0	0	1	1
275.0	0	1	1
278.0	0	1	1
282.0	0	1	1
288.0	0	1	1
290.0	0	1	1
294.0	0	1	1
301.0	0	1	1
303.0	0	1	1
305.0	0	1	1
317.0	0	1	1
326.0	0	1	1
330.0	0	1	1
333.0	0	1	1
337.0	0	1	1
340.0	0	1	1
346.0	0	1	1
350.0	0	1	1
359.0	0	2	2
361.0	0	1	1
363.0	0	1	1
364.0	0	1	1
371.0	0	1	1
387.0	0	1	1
396.0	0	1	1
398.0	0	1	1
412.0	0	1	1
418.0	0	1	1
422.0	0	1	1
429.0	0	1	1
503.0	0	1	1
517.0	0	1	1
535.0	0	1	1
539.0	0	1	1
559.0	0	2	2
586.0	0	1	1
606.0	0	1	1
690.0	0	1	1
718.0	0	1	1
719.0	0	1	1
729.0	0	1	1
749.0	0	1	1
820.0	0	1	1
872.0	0	1	1
873.0	0	1	1
941.0	0	1	1
1210.0	0	1	1
1415.0	0	1	1
1662.0	0	1	1
2459.0	0	1	1