## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Vir_Cha_1_2012-07-18/US_Vir_Cha_1_2012-07-18.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Vir_Cha_1_2012-07-18/US_Vir_Cha_1_2012-07-18.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Vir_Cha_1_2012-07-18/US_Vir_Cha_1_2012-07-18.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 18:21:48 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	7432827	42714208	0	0	3099447	111267	0	0.035774	8184518918

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	42305610	42305610
2.0	1.994795	21242	21242
3.0	2.984411	1285	1285
4.0	3.968876	378	378
5.0	4.948217	218	218
6.0	5.92246	177	177
7.0	6.891632	110	110
8.0	7.855759	87	87
9.0	8.814867	63	63
10.0	9.768983	49	49
11.0	10.718133	35	35
12.0	11.662341	41	41
13.0	12.601635	26	26
14.0	13.53604	20	20
15.0	14.465581	14	14
16.0	15.390283	15	15
17.0	16.310172	21	21
18.0	17.225272	15	15
19.0	18.135609	6	6
20.0	19.041208	4	4
21.0	19.942093	7	7
22.0	20.838288	6	6
23.0	21.729818	8	8
24.0	22.616708	9	9
25.0	23.498981	5	5
26.0	24.376661	4	4
27.0	25.249773	7	7
28.0	26.118341	6	6
29.0	26.982387	1	1
30.0	27.841935	5	5
31.0	28.697009	6	6
32.0	29.547632	3	3
33.0	30.393828	9	9
34.0	31.235619	5	5
35.0	32.073028	6	6
36.0	32.906078	1	1
37.0	33.734791	3	3
38.0	34.559191	4	4
39.0	35.3793	6	6
40.0	36.19514	5	5
41.0	37.006733	0	0
42.0	37.814102	1	1
43.0	38.617268	5	5
44.0	39.416253	6	6
45.0	40.211079	5	5
46.0	41.001768	3	3
47.0	41.788341	1	1
48.0	42.57082	4	4
49.0	43.349226	1	1
50.0	44.12358	2	2
51.0	44.893903	3	3
52.0	45.660216	1	1
53.0	46.422541	2	2
54.0	47.180897	4	4
55.0	47.935306	2	2
56.0	48.685788	2	2
57.0	49.432364	2	2
58.0	50.175053	1	1
59.0	50.913876	1	1
60.0	51.648854	0	0
61.0	52.380006	1	1
62.0	53.107352	1	1
63.0	53.830912	3	3
64.0	54.550705	1	1
65.0	55.266752	2	2
66.0	55.979071	0	0
67.0	56.687683	1	1
68.0	57.392606	3	3
69.0	58.09386	1	1
70.0	58.791464	5	5
71.0	59.485436	2	2
72.0	60.175796	0	0
73.0	60.862562	3	3
74.0	61.545754	0	0
75.0	62.225389	2	2
76.0	62.901487	3	3
77.0	63.574066	2	2
78.0	64.243143	0	0
79.0	64.908738	2	2
80.0	65.570868	0	0
81.0	66.229551	0	0
82.0	66.884806	0	0
83.0	67.53665	0	0
84.0	68.185101	4	4
85.0	68.830176	3	3
86.0	69.471894	2	2
87.0	70.110272	3	3
88.0	70.745326	1	1
89.0	71.377075	2	2
90.0	72.005535	1	1
91.0	72.630724	0	0
92.0	73.252659	0	0
93.0	73.871356	4	4
94.0	74.486833	1	1
95.0	75.099106	1	1
96.0	75.708192	1	1
97.0	76.314108	1	1
98.0	76.916869	2	2
99.0	77.516493	1	1
100.0	78.112996	0	0
101.0	0	3	3
105.0	0	2	2
106.0	0	3	3
108.0	0	3	3
110.0	0	1	1
115.0	0	1	1
117.0	0	1	1
118.0	0	1	1
119.0	0	2	2
121.0	0	1	1
123.0	0	1	1
125.0	0	2	2
126.0	0	1	1
128.0	0	1	1
129.0	0	1	1
132.0	0	1	1
133.0	0	1	1
134.0	0	2	2
144.0	0	1	1
145.0	0	1	1
147.0	0	1	1
152.0	0	1	1
153.0	0	2	2
155.0	0	1	1
156.0	0	1	1
163.0	0	1	1
164.0	0	2	2
166.0	0	2	2
167.0	0	1	1
173.0	0	1	1
175.0	0	1	1
180.0	0	1	1
182.0	0	1	1
184.0	0	1	1
196.0	0	1	1
202.0	0	1	1
208.0	0	1	1
210.0	0	1	1
215.0	0	1	1
222.0	0	1	1
224.0	0	1	1
226.0	0	1	1
228.0	0	1	1
229.0	0	1	1
237.0	0	1	1
238.0	0	1	1
239.0	0	1	1
241.0	0	1	1
288.0	0	1	1
290.0	0	1	1
302.0	0	1	1
306.0	0	1	1
309.0	0	1	1
312.0	0	1	1
323.0	0	1	1
352.0	0	1	1
385.0	0	2	2
395.0	0	1	1
464.0	0	1	1
480.0	0	1	1
482.0	0	1	1
597.0	0	1	1
608.0	0	1	1
616.0	0	1	1
622.0	0	1	1
640.0	0	1	1
767.0	0	1	1
836.0	0	1	1
923.0	0	1	1
1080.0	0	1	1
1194.0	0	1	1
1244.0	0	1	1
1590.0	0	1	1
1724.0	0	1	1
2181.0	0	1	1
2260.0	0	1	1
4421.0	0	1	1
6118.0	0	1	1
6312.0	0	1	1
6442.0	0	1	1
15308.0	0	1	1