## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[./pipeline_output_destplus/AU_Que_Yep_5_2014-05-16/AU_Que_Yep_5_2014-05-16.sorted_merged.bam] OUTPUT=./pipeline_output_destplus/AU_Que_Yep_5_2014-05-16/AU_Que_Yep_5_2014-05-16.dedup.bam METRICS_FILE=./pipeline_output_destplus/AU_Que_Yep_5_2014-05-16/AU_Que_Yep_5_2014-05-16.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 13 21:36:48 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	394589	18056839	0	0	225467	9073332	0	0.503232	11236156

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	1068	1068
2.0	1.200482	8639560	8639560
3.0	1.240675	23	23
4.0	1.248733	138057	138057
5.0	1.250349	3	3
6.0	1.250673	2978	2978
7.0	1.250738	0	0
8.0	1.250751	379	379
9.0	1.250753	0	0
10.0	1.250754	101	101
11.0	1.250754	0	0
12.0	1.250754	29	29
13.0	1.250754	0	0
14.0	1.250754	26	26
15.0	1.250754	0	0
16.0	1.250754	8	8
17.0	1.250754	0	0
18.0	1.250754	2	2
19.0	1.250754	0	0
20.0	1.250754	5	5
21.0	1.250754	0	0
22.0	1.250754	2	2
23.0	1.250754	0	0
24.0	1.250754	0	0
25.0	1.250754	0	0
26.0	1.250754	3	3
27.0	1.250754	0	0
28.0	1.250754	1	1
29.0	1.250754	0	0
30.0	1.250754	0	0
31.0	1.250754	0	0
32.0	1.250754	0	0
33.0	1.250754	0	0
34.0	1.250754	0	0
35.0	1.250754	0	0
36.0	1.250754	0	0
37.0	1.250754	0	0
38.0	1.250754	0	0
39.0	1.250754	0	0
40.0	1.250754	0	0
41.0	1.250754	0	0
42.0	1.250754	1	1
43.0	1.250754	0	0
44.0	1.250754	0	0
45.0	1.250754	0	0
46.0	1.250754	0	0
47.0	1.250754	0	0
48.0	1.250754	0	0
49.0	1.250754	0	0
50.0	1.250754	0	0
51.0	1.250754	0	0
52.0	1.250754	0	0
53.0	1.250754	0	0
54.0	1.250754	0	0
55.0	1.250754	0	0
56.0	1.250754	0	0
57.0	1.250754	0	0
58.0	1.250754	0	0
59.0	1.250754	0	0
60.0	1.250754	0	0
61.0	1.250754	0	0
62.0	1.250754	0	0
63.0	1.250754	0	0
64.0	1.250754	0	0
65.0	1.250754	0	0
66.0	1.250754	0	0
67.0	1.250754	0	0
68.0	1.250754	0	0
69.0	1.250754	0	0
70.0	1.250754	0	0
71.0	1.250754	0	0
72.0	1.250754	0	0
73.0	1.250754	0	0
74.0	1.250754	0	0
75.0	1.250754	0	0
76.0	1.250754	0	0
77.0	1.250754	0	0
78.0	1.250754	0	0
79.0	1.250754	0	0
80.0	1.250754	0	0
81.0	1.250754	0	0
82.0	1.250754	0	0
83.0	1.250754	0	0
84.0	1.250754	0	0
85.0	1.250754	0	0
86.0	1.250754	0	0
87.0	1.250754	0	0
88.0	1.250754	0	0
89.0	1.250754	0	0
90.0	1.250754	0	0
91.0	1.250754	0	0
92.0	1.250754	0	0
93.0	1.250754	0	0
94.0	1.250754	0	0
95.0	1.250754	0	0
96.0	1.250754	0	0
97.0	1.250754	0	0
98.0	1.250754	0	0
99.0	1.250754	0	0
100.0	1.250754	0	0