## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/US_Tex_Sto_0_2013-09-15/US_Tex_Sto_0_2013-09-15.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/US_Tex_Sto_0_2013-09-15/US_Tex_Sto_0_2013-09-15.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/RECENT_OUTPUTS/US_Tex_Sto_0_2013-09-15/US_Tex_Sto_0_2013-09-15.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: Tue Apr 25 06:34:53 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	2860981	72099767	0	0	1670316	1376526	0	0.030079	1864112589

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	68738707	68738707
2.0	1.962061	1126681	1126681
3.0	2.887621	60498	60498
4.0	3.778067	14820	14820
5.0	4.634729	6054	6054
6.0	5.458891	2889	2889
7.0	6.251784	1557	1557
8.0	7.014595	979	979
9.0	7.748466	632	632
10.0	8.454494	390	390
11.0	9.133736	270	270
12.0	9.787208	215	215
13.0	10.415887	149	149
14.0	11.020715	122	122
15.0	11.602596	88	88
16.0	12.162401	74	74
17.0	12.700968	49	49
18.0	13.219101	40	40
19.0	13.717577	29	29
20.0	14.197141	19	19
21.0	14.65851	31	31
22.0	15.102376	23	23
23.0	15.529401	14	14
24.0	15.940226	21	21
25.0	16.335464	14	14
26.0	16.715707	14	14
27.0	17.081523	7	7
28.0	17.433461	6	6
29.0	17.772047	11	11
30.0	18.097787	7	7
31.0	18.411168	4	4
32.0	18.71266	6	6
33.0	19.002714	5	5
34.0	19.281763	6	6
35.0	19.550225	8	8
36.0	19.808502	1	1
37.0	20.05698	7	7
38.0	20.296031	7	7
39.0	20.526013	3	3
40.0	20.747269	3	3
41.0	20.960131	0	0
42.0	21.164917	1	1
43.0	21.361934	2	2
44.0	21.551475	1	1
45.0	21.733826	2	2
46.0	21.909259	1	1
47.0	22.078035	1	1
48.0	22.240409	2	2
49.0	22.396622	2	2
50.0	22.546908	1	1
51.0	22.691493	2	2
52.0	22.830592	3	3
53.0	22.964414	1	1
54.0	23.093159	0	0
55.0	23.217019	0	0
56.0	23.33618	0	0
57.0	23.450821	1	1
58.0	23.561112	1	1
59.0	23.667218	0	0
60.0	23.769299	1	1
61.0	23.867507	2	2
62.0	23.961989	0	0
63.0	24.052886	2	2
64.0	24.140335	0	0
65.0	24.224466	1	1
66.0	24.305406	0	0
67.0	24.383274	0	0
68.0	24.458188	0	0
69.0	24.53026	0	0
70.0	24.599598	1	1
71.0	24.666305	1	1
72.0	24.730481	2	2
73.0	24.792222	0	0
74.0	24.851621	1	1
75.0	24.908766	0	0
76.0	24.963744	0	0
77.0	25.016635	1	1
78.0	25.06752	0	0
79.0	25.116474	0	0
80.0	25.163571	0	0
81.0	25.208882	0	0
82.0	25.252473	0	0
83.0	25.29441	0	0
84.0	25.334756	0	0
85.0	25.373572	0	0
86.0	25.410915	0	0
87.0	25.446841	1	1
88.0	25.481404	0	0
89.0	25.514656	0	0
90.0	25.546646	1	1
91.0	25.577423	0	0
92.0	25.607031	0	0
93.0	25.635517	1	1
94.0	25.662922	0	0
95.0	25.689287	0	0
96.0	25.714652	0	0
97.0	25.739054	0	0
98.0	25.762531	1	1
99.0	25.785117	0	0
100.0	25.806846	0	0
118.0	0	1	1
124.0	0	1	1
129.0	0	1	1
159.0	0	1	1