## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/test_pipeline/small_variant_caller/interim/A/mapped/A-2.sorted.bam] OUTPUT=/test_pipeline/small_variant_caller/interim/A/dedup/A-2.bam METRICS_FILE=/test_pipeline/small_variant_caller/analysis/A/qc/dedup/A-2.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 19:40:06 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	196	4401	58	234	9	115	0	0.026561	82738

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	4222	4222
2.0	1.948198	42	42
3.0	2.847277	8	8
4.0	3.699782	8	8
5.0	4.508125	3	3
6.0	5.274595	1	1
7.0	6.00136	0	0
8.0	6.690477	1	1
9.0	7.343896	0	0
10.0	7.963467	1	1
11.0	8.550942	0	0
12.0	9.107986	0	0
13.0	9.636173	0	0
14.0	10.136999	0	0
15.0	10.611882	0	0
16.0	11.062164	0	0
17.0	11.489121	0	0
18.0	11.89396	0	0
19.0	12.277829	0	0
20.0	12.641811	0	0
21.0	12.986939	0	0
22.0	13.314189	0	0
23.0	13.624486	0	0
24.0	13.91871	0	0
25.0	14.197691	0	0
26.0	14.462222	0	0
27.0	14.713048	0	0
28.0	14.950882	0	0
29.0	15.176395	0	0
30.0	15.390226	0	0
31.0	15.592981	0	0
32.0	15.785232	0	0
33.0	15.967524	0	0
34.0	16.140373	0	0
35.0	16.304268	0	0
36.0	16.459673	0	0
37.0	16.607028	0	0
38.0	16.74675	0	0
39.0	16.879233	0	0
40.0	17.004854	0	0
41.0	17.123967	0	0
42.0	17.23691	0	0
43.0	17.344002	0	0
44.0	17.445547	0	0
45.0	17.541832	0	0
46.0	17.633128	0	0
47.0	17.719696	0	0
48.0	17.801779	0	0
49.0	17.87961	0	0
50.0	17.953409	0	0
51.0	18.023385	0	0
52.0	18.089736	0	0
53.0	18.15265	0	0
54.0	18.212305	0	0
55.0	18.26887	0	0
56.0	18.322505	0	0
57.0	18.373361	0	0
58.0	18.421583	0	0
59.0	18.467307	0	0
60.0	18.510662	0	0
61.0	18.551771	0	0
62.0	18.590751	0	0
63.0	18.627711	0	0
64.0	18.662757	0	0
65.0	18.695988	0	0
66.0	18.727497	0	0
67.0	18.757374	0	0
68.0	18.785703	0	0
69.0	18.812564	0	0
70.0	18.838035	0	0
71.0	18.862185	0	0
72.0	18.885085	0	0
73.0	18.906798	0	0
74.0	18.927387	0	0
75.0	18.946909	0	0
76.0	18.96542	0	0
77.0	18.982972	0	0
78.0	18.999615	0	0
79.0	19.015395	0	0
80.0	19.030358	0	0
81.0	19.044546	0	0
82.0	19.057999	0	0
83.0	19.070755	0	0
84.0	19.082851	0	0
85.0	19.094319	0	0
86.0	19.105194	0	0
87.0	19.115505	0	0
88.0	19.125282	0	0
89.0	19.134553	0	0
90.0	19.143344	0	0
91.0	19.151679	0	0
92.0	19.159582	0	0
93.0	19.167076	0	0
94.0	19.174182	0	0
95.0	19.180919	0	0
96.0	19.187308	0	0
97.0	19.193366	0	0
98.0	19.199109	0	0
99.0	19.204556	0	0
100.0	19.20972	0	0

