## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/test_pipeline/small_variant_caller/interim/A/mapped/A-1.sorted.bam] OUTPUT=/test_pipeline/small_variant_caller/interim/A/dedup/A-1.bam METRICS_FILE=/test_pipeline/small_variant_caller/analysis/A/qc/dedup/A-1.metrics.txt REMOVE_DUPLICATES=true TMP_DIR=[/tmp]    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 VALIDATION_STRINGENCY=STRICT 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 Apr 02 19:39:58 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	198	4342	52	240	8	137	0	0.03175	67351

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	4136	4136
2.0	1.937566	39	39
3.0	2.816595	14	14
4.0	3.640743	7	7
5.0	4.413437	3	3
6.0	5.137888	0	0
7.0	5.817108	5	5
8.0	6.453922	1	1
9.0	7.050977	0	0
10.0	7.610755	0	0
11.0	8.135584	0	0
12.0	8.627646	0	0
13.0	9.088987	0	0
14.0	9.521524	0	0
15.0	9.927056	0	0
16.0	10.307269	0	0
17.0	10.663744	0	0
18.0	10.997962	0	0
19.0	11.311314	0	0
20.0	11.605102	0	0
21.0	11.880548	0	0
22.0	12.138796	0	0
23.0	12.380921	0	0
24.0	12.607929	0	0
25.0	12.820765	0	0
26.0	13.020311	0	0
27.0	13.2074	0	0
28.0	13.382807	0	0
29.0	13.547264	0	0
30.0	13.701452	0	0
31.0	13.846014	0	0
32.0	13.981551	0	0
33.0	14.108625	0	0
34.0	14.227765	0	0
35.0	14.339467	0	0
36.0	14.444195	0	0
37.0	14.542385	0	0
38.0	14.634444	0	0
39.0	14.720755	0	0
40.0	14.801678	0	0
41.0	14.877548	0	0
42.0	14.948682	0	0
43.0	15.015374	0	0
44.0	15.077903	0	0
45.0	15.136527	0	0
46.0	15.191491	0	0
47.0	15.243024	0	0
48.0	15.291339	0	0
49.0	15.336638	0	0
50.0	15.379109	0	0
51.0	15.418928	0	0
52.0	15.456261	0	0
53.0	15.491263	0	0
54.0	15.524079	0	0
55.0	15.554847	0	0
56.0	15.583694	0	0
57.0	15.61074	0	0
58.0	15.636097	0	0
59.0	15.659871	0	0
60.0	15.682161	0	0
61.0	15.703059	0	0
62.0	15.722653	0	0
63.0	15.741023	0	0
64.0	15.758246	0	0
65.0	15.774394	0	0
66.0	15.789534	0	0
67.0	15.803728	0	0
68.0	15.817036	0	0
69.0	15.829514	0	0
70.0	15.841212	0	0
71.0	15.85218	0	0
72.0	15.862463	0	0
73.0	15.872104	0	0
74.0	15.881144	0	0
75.0	15.889618	0	0
76.0	15.897564	0	0
77.0	15.905014	0	0
78.0	15.911998	0	0
79.0	15.918547	0	0
80.0	15.924687	0	0
81.0	15.930443	0	0
82.0	15.93584	0	0
83.0	15.9409	0	0
84.0	15.945644	0	0
85.0	15.950092	0	0
86.0	15.954262	0	0
87.0	15.958172	0	0
88.0	15.961837	0	0
89.0	15.965274	0	0
90.0	15.968496	0	0
91.0	15.971517	0	0
92.0	15.97435	0	0
93.0	15.977006	0	0
94.0	15.979495	0	0
95.0	15.98183	0	0
96.0	15.984018	0	0
97.0	15.98607	0	0
98.0	15.987994	0	0
99.0	15.989798	0	0
100.0	15.991489	0	0

