## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Tuo_1_2013-05-14/US_Cal_Tuo_1_2013-05-14.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Tuo_1_2013-05-14/US_Cal_Tuo_1_2013-05-14.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Tuo_1_2013-05-14/US_Cal_Tuo_1_2013-05-14.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 17:57:08 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	2658688	41170911	0	0	1052811	2046239	0	0.060532	400344788

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	36154260	36154260
2.0	1.902273	1764706	1764706
3.0	2.716368	79473	79473
4.0	3.450905	6380	6380
5.0	4.113657	1567	1567
6.0	4.711639	770	770
7.0	5.251183	394	394
8.0	5.737998	265	265
9.0	6.177238	182	182
10.0	6.573553	141	141
11.0	6.931136	96	96
12.0	7.253774	110	110
13.0	7.544881	89	89
14.0	7.807539	58	58
15.0	8.044528	58	58
16.0	8.258357	62	62
17.0	8.451289	48	48
18.0	8.625366	41	41
19.0	8.782431	46	46
20.0	8.924147	28	28
21.0	9.052013	48	48
22.0	9.167383	35	35
23.0	9.271478	29	29
24.0	9.3654	23	23
25.0	9.450143	31	31
26.0	9.526605	23	23
27.0	9.595594	19	19
28.0	9.657841	24	24
29.0	9.714005	24	24
30.0	9.76468	17	17
31.0	9.810403	18	18
32.0	9.851658	14	14
33.0	9.88888	22	22
34.0	9.922465	19	19
35.0	9.952768	8	8
36.0	9.98011	16	16
37.0	10.004779	12	12
38.0	10.027038	11	11
39.0	10.047121	11	11
40.0	10.065241	8	8
41.0	10.081591	5	5
42.0	10.096343	9	9
43.0	10.109653	14	14
44.0	10.121663	6	6
45.0	10.132498	11	11
46.0	10.142275	7	7
47.0	10.151097	7	7
48.0	10.159056	5	5
49.0	10.166237	13	13
50.0	10.172717	5	5
51.0	10.178563	7	7
52.0	10.183838	4	4
53.0	10.188598	10	10
54.0	10.192892	5	5
55.0	10.196767	7	7
56.0	10.200263	5	5
57.0	10.203417	2	2
58.0	10.206264	5	5
59.0	10.208832	7	7
60.0	10.211149	3	3
61.0	10.213239	4	4
62.0	10.215125	4	4
63.0	10.216827	1	1
64.0	10.218363	1	1
65.0	10.219748	3	3
66.0	10.220999	3	3
67.0	10.222127	1	1
68.0	10.223144	3	3
69.0	10.224063	2	2
70.0	10.224891	0	0
71.0	10.225639	0	0
72.0	10.226313	3	3
73.0	10.226922	4	4
74.0	10.227471	1	1
75.0	10.227966	1	1
76.0	10.228413	2	2
77.0	10.228817	4	4
78.0	10.229181	0	0
79.0	10.229509	0	0
80.0	10.229805	2	2
81.0	10.230072	0	0
82.0	10.230314	2	2
83.0	10.230531	1	1
84.0	10.230728	2	2
85.0	10.230905	0	0
86.0	10.231065	1	1
87.0	10.231209	0	0
88.0	10.231339	1	1
89.0	10.231456	2	2
90.0	10.231562	0	0
91.0	10.231658	4	4
92.0	10.231744	2	2
93.0	10.231822	1	1
94.0	10.231892	1	1
95.0	10.231956	1	1
96.0	10.232013	3	3
97.0	10.232064	2	2
98.0	10.232111	1	1
99.0	10.232153	0	0
100.0	10.232191	0	0
102.0	0	1	1
103.0	0	1	1
104.0	0	1	1
105.0	0	2	2
107.0	0	2	2
109.0	0	1	1
113.0	0	2	2
118.0	0	2	2
122.0	0	1	1
124.0	0	1	1
125.0	0	2	2
126.0	0	1	1
131.0	0	2	2
132.0	0	1	1
137.0	0	1	1
142.0	0	1	1
143.0	0	1	1
146.0	0	1	1
148.0	0	1	1
149.0	0	1	1
151.0	0	1	1
157.0	0	1	1
161.0	0	1	1
162.0	0	1	1
165.0	0	1	1
174.0	0	1	1
188.0	0	1	1
189.0	0	1	1
195.0	0	2	2
199.0	0	1	1
201.0	0	1	1
203.0	0	1	1
206.0	0	1	1
213.0	0	1	1
214.0	0	1	1
217.0	0	1	1
218.0	0	1	1
221.0	0	1	1
223.0	0	1	1
225.0	0	1	1
233.0	0	1	1
234.0	0	1	1
235.0	0	1	1
242.0	0	1	1
248.0	0	1	1
256.0	0	1	1
259.0	0	1	1
264.0	0	1	1
265.0	0	1	1
273.0	0	1	1
284.0	0	1	1
293.0	0	1	1
303.0	0	1	1
307.0	0	1	1
337.0	0	1	1
342.0	0	1	1
344.0	0	1	1
365.0	0	1	1
378.0	0	1	1
381.0	0	1	1
382.0	0	1	1
383.0	0	1	1
392.0	0	1	1
406.0	0	1	1
416.0	0	1	1
422.0	0	1	1
429.0	0	1	1
432.0	0	1	1
448.0	0	1	1
453.0	0	1	1
455.0	0	1	1
464.0	0	1	1
481.0	0	1	1
500.0	0	1	1
519.0	0	1	1
522.0	0	1	1
593.0	0	1	1
631.0	0	1	1
671.0	0	1	1
678.0	0	1	1
733.0	0	1	1
749.0	0	1	1
785.0	0	1	1
855.0	0	1	1
921.0	0	1	1
941.0	0	1	1
978.0	0	1	1
984.0	0	1	1
990.0	0	1	1
1028.0	0	1	1
1094.0	0	1	1
1104.0	0	1	1
1256.0	0	1	1
1323.0	0	1	1
1333.0	0	1	1
1545.0	0	1	1
1608.0	0	1	1
1624.0	0	1	1
2014.0	0	1	1
2034.0	0	1	1
2282.0	0	1	1
2526.0	0	1	1
3829.0	0	1	1