## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Mas_Lan_1_2012-07-28/US_Mas_Lan_1_2012-07-28.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Mas_Lan_1_2012-07-28/US_Mas_Lan_1_2012-07-28.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Mas_Lan_1_2012-07-28/US_Mas_Lan_1_2012-07-28.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 17:23:53 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	4241889	33503946	0	0	1590007	141865	0	0.026298	3945100852

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	33050053	33050053
2.0	1.991543	10217	10217
3.0	2.974702	605	605
4.0	3.949546	242	242
5.0	4.916146	176	176
6.0	5.874572	123	123
7.0	6.824894	77	77
8.0	7.767178	77	77
9.0	8.701495	72	72
10.0	9.62791	58	58
11.0	10.54649	28	28
12.0	11.457303	26	26
13.0	12.360413	18	18
14.0	13.255887	19	19
15.0	14.143787	16	16
16.0	15.024179	15	15
17.0	15.897126	12	12
18.0	16.76269	12	12
19.0	17.620935	9	9
20.0	18.471922	11	11
21.0	19.315713	7	7
22.0	20.152368	4	4
23.0	20.981948	8	8
24.0	21.804512	7	7
25.0	22.62012	5	5
26.0	23.428831	5	5
27.0	24.230703	8	8
28.0	25.025794	5	5
29.0	25.814162	3	3
30.0	26.595862	3	3
31.0	27.370952	5	5
32.0	28.139487	3	3
33.0	28.901523	4	4
34.0	29.657115	4	4
35.0	30.406317	1	1
36.0	31.149183	4	4
37.0	31.885768	3	3
38.0	32.616123	4	4
39.0	33.340302	6	6
40.0	34.058357	3	3
41.0	34.770339	3	3
42.0	35.476301	2	2
43.0	36.176293	1	1
44.0	36.870365	4	4
45.0	37.558567	1	1
46.0	38.24095	3	3
47.0	38.917562	3	3
48.0	39.588453	0	0
49.0	40.25367	3	3
50.0	40.913261	5	5
51.0	41.567275	1	1
52.0	42.215757	3	3
53.0	42.858756	3	3
54.0	43.496317	2	2
55.0	44.128487	1	1
56.0	44.755311	0	0
57.0	45.376834	6	6
58.0	45.993101	1	1
59.0	46.604156	3	3
60.0	47.210044	0	0
61.0	47.810808	3	3
62.0	48.406492	1	1
63.0	48.997139	0	0
64.0	49.58279	3	3
65.0	50.163489	2	2
66.0	50.739277	0	0
67.0	51.310196	0	0
68.0	51.876287	0	0
69.0	52.437591	3	3
70.0	52.994148	0	0
71.0	53.545998	2	2
72.0	54.093182	4	4
73.0	54.635739	1	1
74.0	55.173707	1	1
75.0	55.707126	2	2
76.0	56.236034	4	4
77.0	56.760469	1	1
78.0	57.280469	0	0
79.0	57.796072	1	1
80.0	58.307315	1	1
81.0	58.814234	1	1
82.0	59.316866	0	0
83.0	59.815248	1	1
84.0	60.309415	0	0
85.0	60.799404	1	1
86.0	61.285248	2	2
87.0	61.766984	0	0
88.0	62.244647	2	2
89.0	62.718269	2	2
90.0	63.187887	3	3
91.0	63.653533	1	1
92.0	64.115242	0	0
93.0	64.573046	0	0
94.0	65.026978	1	1
95.0	65.477072	1	1
96.0	65.92336	2	2
97.0	66.365873	2	2
98.0	66.804645	2	2
99.0	67.239705	2	2
100.0	67.671087	1	1
101.0	0	3	3
102.0	0	3	3
105.0	0	1	1
109.0	0	1	1
110.0	0	1	1
112.0	0	1	1
115.0	0	1	1
117.0	0	2	2
118.0	0	1	1
120.0	0	1	1
122.0	0	2	2
124.0	0	1	1
126.0	0	2	2
127.0	0	3	3
134.0	0	3	3
135.0	0	2	2
138.0	0	1	1
141.0	0	2	2
144.0	0	1	1
146.0	0	1	1
155.0	0	1	1
159.0	0	1	1
161.0	0	2	2
162.0	0	1	1
169.0	0	1	1
170.0	0	1	1
182.0	0	1	1
183.0	0	1	1
185.0	0	1	1
199.0	0	3	3
201.0	0	1	1
204.0	0	1	1
206.0	0	1	1
213.0	0	1	1
215.0	0	1	1
216.0	0	1	1
226.0	0	1	1
229.0	0	1	1
235.0	0	1	1
245.0	0	1	1
250.0	0	1	1
263.0	0	1	1
274.0	0	1	1
290.0	0	1	1
291.0	0	1	1
309.0	0	1	1
314.0	0	1	1
335.0	0	1	1
350.0	0	1	1
492.0	0	1	1
505.0	0	1	1
551.0	0	1	1
573.0	0	1	1
582.0	0	1	1
693.0	0	1	1
720.0	0	1	1
781.0	0	1	1
865.0	0	1	1
908.0	0	1	1
1000.0	0	1	1
1065.0	0	1	1
1093.0	0	1	1
1183.0	0	1	1
1263.0	0	1	1
1648.0	0	1	1
1669.0	0	1	1
1802.0	0	1	1
1878.0	0	1	1
2168.0	0	1	1
2360.0	0	1	1
2963.0	0	1	1
3415.0	0	1	1
3672.0	0	1	1
8182.0	0	1	1
9919.0	0	1	1
11405.0	0	1	1
12187.0	0	1	1
28437.0	0	1	1