## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/pipeline_output//UA_Cho_15_24/UA_Cho_15_24.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Cho_15_24/UA_Cho_15_24.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/pipeline_output/UA_Cho_15_24/UA_Cho_15_24.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: Sun Jun 07 12:42:54 UTC 2020

## 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	13110585	23746737	0	0	5197739	5782730	0	0.276602	40471052

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	13227999	13227999
2.0	1.556127	3383974	3383974
3.0	1.865404	811065	811065
4.0	2.037402	181532	181532
5.0	2.133054	38504	38504
6.0	2.186249	8076	8076
7.0	2.215832	1815	1815
8.0	2.232284	506	506
9.0	2.241433	246	246
10.0	2.246522	131	131
11.0	2.249351	120	120
12.0	2.250925	107	107
13.0	2.2518	70	70
14.0	2.252287	72	72
15.0	2.252558	55	55
16.0	2.252708	43	43
17.0	2.252792	54	54
18.0	2.252838	35	35
19.0	2.252864	39	39
20.0	2.252879	30	30
21.0	2.252887	24	24
22.0	2.252891	17	17
23.0	2.252894	24	24
24.0	2.252895	26	26
25.0	2.252896	14	14
26.0	2.252896	13	13
27.0	2.252896	14	14
28.0	2.252897	14	14
29.0	2.252897	15	15
30.0	2.252897	13	13
31.0	2.252897	6	6
32.0	2.252897	7	7
33.0	2.252897	7	7
34.0	2.252897	6	6
35.0	2.252897	11	11
36.0	2.252897	5	5
37.0	2.252897	6	6
38.0	2.252897	7	7
39.0	2.252897	8	8
40.0	2.252897	4	4
41.0	2.252897	2	2
42.0	2.252897	5	5
43.0	2.252897	2	2
44.0	2.252897	4	4
45.0	2.252897	6	6
46.0	2.252897	5	5
47.0	2.252897	4	4
48.0	2.252897	3	3
49.0	2.252897	3	3
50.0	2.252897	3	3
51.0	2.252897	1	1
52.0	2.252897	3	3
53.0	2.252897	2	2
54.0	2.252897	5	5
55.0	2.252897	4	4
56.0	2.252897	2	2
57.0	2.252897	2	2
58.0	2.252897	2	2
59.0	2.252897	0	0
60.0	2.252897	0	0
61.0	2.252897	1	1
62.0	2.252897	1	1
63.0	2.252897	1	1
64.0	2.252897	1	1
65.0	2.252897	2	2
66.0	2.252897	1	1
67.0	2.252897	0	0
68.0	2.252897	1	1
69.0	2.252897	2	2
70.0	2.252897	0	0
71.0	2.252897	3	3
72.0	2.252897	0	0
73.0	2.252897	0	0
74.0	2.252897	0	0
75.0	2.252897	2	2
76.0	2.252897	0	0
77.0	2.252897	0	0
78.0	2.252897	0	0
79.0	2.252897	1	1
80.0	2.252897	0	0
81.0	2.252897	0	0
82.0	2.252897	0	0
83.0	2.252897	1	1
84.0	2.252897	0	0
85.0	2.252897	1	1
86.0	2.252897	0	0
87.0	2.252897	1	1
88.0	2.252897	1	1
89.0	2.252897	1	1
90.0	2.252897	0	0
91.0	2.252897	0	0
92.0	2.252897	0	0
93.0	2.252897	0	0
94.0	2.252897	0	0
95.0	2.252897	0	0
96.0	2.252897	1	1
97.0	2.252897	0	0
98.0	2.252897	0	0
99.0	2.252897	0	0
100.0	2.252897	0	0
103.0	0	1	1
107.0	0	1	1
113.0	0	1	1
126.0	0	1	1
137.0	0	1	1
167.0	0	1	1
174.0	0	1	1