## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[HCC1395_Exome_chr21_namesorted_picard.bam] OUTPUT=HCC1395_Exome_chr21_namesorted_picard_mrkdup.bam METRICS_FILE=HCC1395_Exome_chr21_mrk_dup_metrics.txt ASSUME_SORT_ORDER=queryname QUIET=true VALIDATION_STRINGENCY=LENIENT COMPRESSION_LEVEL=0    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 REMOVE_DUPLICATES=false 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 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: Thu Nov 14 17:34:29 EST 2024

## 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
Unknown Library	13639	898743	1807	13641	4492	97697	297	0.110366	3838533

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.000293	713400	0	713634
2.0	1.791779	78631	295	78449
3.0	2.418044	8088	1	8046
4.0	2.913579	829	0	820
5.0	3.305672	87	0	86
6.0	3.615918	11	0	11
7.0	3.8614	0	0	0
8.0	4.055639	0	0	0
9.0	4.209331	0	0	0
10.0	4.330941	0	0	0
11.0	4.427165	0	0	0
12.0	4.503302	0	0	0
13.0	4.563546	0	0	0
14.0	4.611214	0	0	0
15.0	4.648932	0	0	0
16.0	4.678776	0	0	0
17.0	4.702391	0	0	0
18.0	4.721076	0	0	0
19.0	4.73586	0	0	0
20.0	4.747558	0	0	0
21.0	4.756815	0	0	0
22.0	4.764139	0	0	0
23.0	4.769934	0	0	0
24.0	4.77452	0	0	0
25.0	4.778148	0	0	0
26.0	4.781019	0	0	0
27.0	4.78329	0	0	0
28.0	4.785088	0	0	0
29.0	4.78651	0	0	0
30.0	4.787635	0	0	0
31.0	4.788526	0	0	0
32.0	4.78923	0	0	0
33.0	4.789788	0	0	0
34.0	4.790229	0	0	0
35.0	4.790578	0	0	0
36.0	4.790854	0	0	0
37.0	4.791073	0	0	0
38.0	4.791245	0	0	0
39.0	4.791382	0	0	0
40.0	4.791491	0	0	0
41.0	4.791576	0	0	0
42.0	4.791644	0	0	0
43.0	4.791698	0	0	0
44.0	4.79174	0	0	0
45.0	4.791774	0	0	0
46.0	4.7918	0	0	0
47.0	4.791821	0	0	0
48.0	4.791838	0	0	0
49.0	4.791851	0	0	0
50.0	4.791861	0	0	0
51.0	4.79187	0	0	0
52.0	4.791876	0	0	0
53.0	4.791881	0	0	0
54.0	4.791885	0	0	0
55.0	4.791889	0	0	0
56.0	4.791891	0	0	0
57.0	4.791893	0	0	0
58.0	4.791895	0	0	0
59.0	4.791896	0	0	0
60.0	4.791897	0	0	0
61.0	4.791898	0	0	0
62.0	4.791898	0	0	0
63.0	4.791899	0	0	0
64.0	4.791899	0	0	0
65.0	4.7919	0	0	0
66.0	4.7919	0	0	0
67.0	4.7919	0	0	0
68.0	4.7919	0	0	0
69.0	4.7919	0	0	0
70.0	4.7919	0	0	0
71.0	4.791901	0	0	0
72.0	4.791901	0	0	0
73.0	4.791901	0	0	0
74.0	4.791901	0	0	0
75.0	4.791901	0	0	0
76.0	4.791901	0	0	0
77.0	4.791901	0	0	0
78.0	4.791901	0	0	0
79.0	4.791901	0	0	0
80.0	4.791901	0	0	0
81.0	4.791901	0	0	0
82.0	4.791901	0	0	0
83.0	4.791901	0	0	0
84.0	4.791901	0	0	0
85.0	4.791901	0	0	0
86.0	4.791901	0	0	0
87.0	4.791901	0	0	0
88.0	4.791901	0	0	0
89.0	4.791901	0	0	0
90.0	4.791901	0	0	0
91.0	4.791901	0	0	0
92.0	4.791901	0	0	0
93.0	4.791901	0	0	0
94.0	4.791901	0	0	0
95.0	4.791901	0	0	0
96.0	4.791901	0	0	0
97.0	4.791901	0	0	0
98.0	4.791901	0	0	0
99.0	4.791901	0	0	0
100.0	4.791901	0	0	0