## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[./pipeline_output_destplus/US_Cal_And_1_2013-10-15/US_Cal_And_1_2013-10-15.sorted_merged.bam] OUTPUT=./pipeline_output_destplus/US_Cal_And_1_2013-10-15/US_Cal_And_1_2013-10-15.dedup.bam METRICS_FILE=./pipeline_output_destplus/US_Cal_And_1_2013-10-15/US_Cal_And_1_2013-10-15.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 21:13:13 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	308600	4802612	0	0	47929	44472	0	0.013806	257718039

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	4627741	4627741
2.0	1.981537	26643	26643
3.0	2.944953	1632	1632
4.0	3.890582	541	541
5.0	4.818752	321	321
6.0	5.729785	179	179
7.0	6.623998	142	142
8.0	7.501702	108	108
9.0	8.363201	75	75
10.0	9.208795	68	68
11.0	10.038777	43	43
12.0	10.853435	37	37
13.0	11.653053	35	35
14.0	12.437907	26	26
15.0	13.208272	24	24
16.0	13.964413	11	11
17.0	14.706594	18	18
18.0	15.435072	16	16
19.0	16.150101	18	18
20.0	16.851928	10	10
21.0	17.540798	11	11
22.0	18.21695	8	8
23.0	18.880618	4	4
24.0	19.532033	8	8
25.0	20.171421	8	8
26.0	20.799005	5	5
27.0	21.415001	9	9
28.0	22.019625	2	2
29.0	22.613086	3	3
30.0	23.19559	5	5
31.0	23.76734	2	2
32.0	24.328533	5	5
33.0	24.879366	2	2
34.0	25.420029	1	1
35.0	25.950709	1	1
36.0	26.471592	4	4
37.0	26.982858	3	3
38.0	27.484685	0	0
39.0	27.977247	1	1
40.0	28.460715	2	2
41.0	28.935257	1	1
42.0	29.401037	3	3
43.0	29.858218	2	2
44.0	30.306958	1	1
45.0	30.747414	2	2
46.0	31.179737	0	0
47.0	31.604079	0	0
48.0	32.020586	2	2
49.0	32.429403	0	0
50.0	32.830673	1	1
51.0	33.224534	2	2
52.0	33.611123	2	2
53.0	33.990575	1	1
54.0	34.363021	3	3
55.0	34.728591	0	0
56.0	35.087412	0	0
57.0	35.439608	1	1
58.0	35.785301	1	1
59.0	36.124612	0	0
60.0	36.457659	0	0
61.0	36.784556	1	1
62.0	37.105418	0	0
63.0	37.420357	0	0
64.0	37.72948	0	0
65.0	38.032897	0	0
66.0	38.330711	0	0
67.0	38.623027	2	2
68.0	38.909947	0	0
69.0	39.191569	0	0
70.0	39.467991	1	1
71.0	39.73931	0	0
72.0	40.00562	0	0
73.0	40.267013	0	0
74.0	40.52358	2	2
75.0	40.77541	0	0
76.0	41.022591	1	1
77.0	41.265208	0	0
78.0	41.503346	0	0
79.0	41.737087	0	0
80.0	41.966513	0	0
81.0	42.191703	1	1
82.0	42.412735	0	0
83.0	42.629686	0	0
84.0	42.842632	0	0
85.0	43.051647	1	1
86.0	43.256802	0	0
87.0	43.45817	0	0
88.0	43.65582	1	1
89.0	43.849821	0	0
90.0	44.04024	0	0
91.0	44.227144	0	0
92.0	44.410597	0	0
93.0	44.590662	1	1
94.0	44.767404	0	0
95.0	44.940882	0	0
96.0	45.111157	0	0
97.0	45.278289	0	0
98.0	45.442335	0	0
99.0	45.603352	0	0
100.0	45.761396	0	0
102.0	0	1	1
104.0	0	2	2
120.0	0	1	1
130.0	0	1	1
143.0	0	1	1