## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates --INPUT aligned.bam --OUTPUT marked_duplicates.bam --METRICS_FILE TP53_1.fastq.gz_markduplicates_metrics.txt --ASSUME_SORT_ORDER queryname --OPTICAL_DUPLICATE_PIXEL_DISTANCE 2500 --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 --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> --MAX_OPTICAL_DUPLICATE_SET_SIZE 300000 --VERBOSITY INFO --QUIET false --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --GA4GH_CLIENT_SECRETS client_secrets.json --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false
## htsjdk.samtools.metrics.StringHeader
# Started on: Thu May 20 16:23:36 UTC 2021

## 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	23	644	0	23	23	631	118	0.980168	13

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1	6	0	6
2.0	1	1	0	1
3.0	1	1	0	1
4.0	1	0	0	0
5.0	1	0	0	0
6.0	1	0	0	0
7.0	1	1	0	1
8.0	1	0	0	0
9.0	1	1	0	1
10.0	1	0	0	0
11.0	1	0	0	0
12.0	1	0	0	0
13.0	1	0	0	0
14.0	1	1	0	1
15.0	1	0	0	0
16.0	1	0	0	0
17.0	1	0	0	0
18.0	1	0	0	0
19.0	1	0	0	0
20.0	1	0	0	0
21.0	1	0	0	0
22.0	1	0	0	0
23.0	1	0	0	0
24.0	1	0	0	0
25.0	1	0	0	0
26.0	1	0	0	0
27.0	1	0	0	0
28.0	1	0	0	0
29.0	1	0	0	0
30.0	1	0	0	0
31.0	1	0	0	0
32.0	1	0	0	0
33.0	1	0	0	0
34.0	1	0	0	0
35.0	1	0	0	0
36.0	1	0	0	0
37.0	1	0	0	0
38.0	1	0	1	0
39.0	1	0	0	0
40.0	1	0	0	0
41.0	1	0	0	0
42.0	1	0	0	0
43.0	1	0	0	0
44.0	1	0	0	0
45.0	1	0	0	0
46.0	1	0	0	0
47.0	1	0	0	0
48.0	1	0	0	0
49.0	1	0	0	0
50.0	1	0	0	0
51.0	1	0	0	0
52.0	1	0	0	0
53.0	1	0	0	0
54.0	1	0	0	0
55.0	1	0	0	0
56.0	1	0	0	0
57.0	1	0	0	0
58.0	1	0	0	0
59.0	1	0	0	0
60.0	1	0	0	0
61.0	1	0	0	0
62.0	1	0	0	0
63.0	1	0	0	0
64.0	1	0	0	0
65.0	1	0	0	0
66.0	1	0	0	0
67.0	1	0	0	0
68.0	1	0	0	0
69.0	1	0	0	0
70.0	1	0	0	0
71.0	1	0	0	0
72.0	1	0	0	0
73.0	1	0	0	0
74.0	1	0	0	0
75.0	1	0	0	0
76.0	1	0	0	0
77.0	1	0	0	0
78.0	1	0	0	0
79.0	1	0	0	0
80.0	1	0	0	0
81.0	1	0	0	0
82.0	1	0	1	0
83.0	1	0	0	0
84.0	1	0	0	0
85.0	1	0	0	0
86.0	1	0	0	0
87.0	1	0	0	0
88.0	1	0	0	0
89.0	1	0	0	0
90.0	1	0	0	0
91.0	1	0	0	0
92.0	1	0	0	0
93.0	1	0	0	0
94.0	1	0	0	0
95.0	1	0	0	0
96.0	1	0	0	0
97.0	1	0	0	0
98.0	1	0	0	0
99.0	1	0	0	0
100.0	1	0	0	0
214.0	0	0	0	1
251.0	0	1	0	0
271.0	0	0	0	1
352.0	0	1	0	0

