## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Pir_Aka_1_2015-07-21/FI_Pir_Aka_1_2015-07-21.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Pir_Aka_1_2015-07-21/FI_Pir_Aka_1_2015-07-21.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/FI_Pir_Aka_1_2015-07-21/FI_Pir_Aka_1_2015-07-21.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 20 08:53:42 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	8892899	27815713	0	0	3701006	2838942	0	0.145354	126829158

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	22036797	22036797
2.0	1.803068	2266397	2266397
3.0	2.447985	212367	212367
4.0	2.965898	21918	21918
5.0	3.381816	3224	3224
6.0	3.715827	1033	1033
7.0	3.98406	628	628
8.0	4.19947	426	426
9.0	4.372458	335	335
10.0	4.511379	261	261
11.0	4.622943	228	228
12.0	4.712535	169	169
13.0	4.784484	148	148
14.0	4.842264	145	145
15.0	4.888666	128	128
16.0	4.925929	103	103
17.0	4.955854	79	79
18.0	4.979886	90	90
19.0	4.999185	76	76
20.0	5.014683	56	56
21.0	5.02713	51	51
22.0	5.037125	63	63
23.0	5.045152	35	35
24.0	5.051598	39	39
25.0	5.056775	48	48
26.0	5.060932	23	23
27.0	5.06427	35	35
28.0	5.066951	30	30
29.0	5.069105	29	29
30.0	5.070834	24	24
31.0	5.072222	33	33
32.0	5.073337	32	32
33.0	5.074233	22	22
34.0	5.074952	15	15
35.0	5.075529	12	12
36.0	5.075993	20	20
37.0	5.076366	15	15
38.0	5.076665	10	10
39.0	5.076905	14	14
40.0	5.077098	11	11
41.0	5.077253	4	4
42.0	5.077377	8	8
43.0	5.077477	14	14
44.0	5.077557	14	14
45.0	5.077622	10	10
46.0	5.077673	11	11
47.0	5.077715	14	14
48.0	5.077748	6	6
49.0	5.077775	9	9
50.0	5.077797	7	7
51.0	5.077814	10	10
52.0	5.077828	4	4
53.0	5.077839	5	5
54.0	5.077848	7	7
55.0	5.077855	4	4
56.0	5.077861	3	3
57.0	5.077866	7	7
58.0	5.077869	1	1
59.0	5.077872	8	8
60.0	5.077875	6	6
61.0	5.077877	6	6
62.0	5.077878	2	2
63.0	5.077879	8	8
64.0	5.07788	5	5
65.0	5.077881	3	3
66.0	5.077882	6	6
67.0	5.077882	3	3
68.0	5.077883	6	6
69.0	5.077883	2	2
70.0	5.077883	5	5
71.0	5.077884	2	2
72.0	5.077884	6	6
73.0	5.077884	3	3
74.0	5.077884	5	5
75.0	5.077884	3	3
76.0	5.077884	2	2
77.0	5.077884	4	4
78.0	5.077884	3	3
79.0	5.077884	4	4
80.0	5.077884	1	1
81.0	5.077884	2	2
82.0	5.077884	2	2
83.0	5.077884	0	0
84.0	5.077884	3	3
85.0	5.077884	1	1
86.0	5.077884	1	1
87.0	5.077884	2	2
88.0	5.077884	3	3
89.0	5.077884	0	0
90.0	5.077884	0	0
91.0	5.077884	1	1
92.0	5.077884	2	2
93.0	5.077884	2	2
94.0	5.077884	2	2
95.0	5.077884	2	2
96.0	5.077884	2	2
97.0	5.077884	2	2
98.0	5.077884	3	3
99.0	5.077884	1	1
100.0	5.077884	0	0
101.0	0	2	2
102.0	0	3	3
104.0	0	1	1
109.0	0	2	2
110.0	0	2	2
112.0	0	2	2
114.0	0	1	1
117.0	0	1	1
119.0	0	2	2
124.0	0	2	2
127.0	0	1	1
129.0	0	1	1
130.0	0	1	1
134.0	0	1	1
145.0	0	1	1
146.0	0	1	1
150.0	0	1	1
151.0	0	1	1
152.0	0	1	1
163.0	0	1	1
165.0	0	1	1
169.0	0	1	1
191.0	0	1	1
196.0	0	1	1
203.0	0	1	1
293.0	0	1	1
307.0	0	1	1
351.0	0	1	1