## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Bar_Bar_1_2012-10-16/ES_Bar_Bar_1_2012-10-16.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Bar_Bar_1_2012-10-16/ES_Bar_Bar_1_2012-10-16.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Bar_Bar_1_2012-10-16/ES_Bar_Bar_1_2012-10-16.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 07:51:17 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	966700	31974706	0	0	249552	157777	0	0.008705	3229291347

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	31445885	31445885
2.0	1.990147	62741	62741
3.0	2.970539	4862	4862
4.0	3.941272	1047	1047
5.0	4.90244	389	389
6.0	5.854138	194	194
7.0	6.79646	142	142
8.0	7.729497	127	127
9.0	8.653341	92	92
10.0	9.568083	84	84
11.0	10.473813	55	55
12.0	11.370618	50	50
13.0	12.258588	39	39
14.0	13.137809	52	52
15.0	14.008367	60	60
16.0	14.870349	50	50
17.0	15.723837	48	48
18.0	16.568916	48	48
19.0	17.405669	45	45
20.0	18.234178	34	34
21.0	19.054524	44	44
22.0	19.866787	31	31
23.0	20.671048	18	18
24.0	21.467384	27	27
25.0	22.255874	21	21
26.0	23.036596	38	38
27.0	23.809626	17	17
28.0	24.575039	14	14
29.0	25.332911	20	20
30.0	26.083315	5	5
31.0	26.826327	24	24
32.0	27.562018	15	15
33.0	28.29046	12	12
34.0	29.011725	19	19
35.0	29.725884	8	8
36.0	30.433007	10	10
37.0	31.133163	9	9
38.0	31.82642	7	7
39.0	32.512847	11	11
40.0	33.192511	9	9
41.0	33.865478	10	10
42.0	34.531815	4	4
43.0	35.191586	8	8
44.0	35.844858	6	6
45.0	36.491693	2	2
46.0	37.132154	9	9
47.0	37.766306	11	11
48.0	38.394209	3	3
49.0	39.015926	9	9
50.0	39.631518	2	2
51.0	40.241044	9	9
52.0	40.844565	2	2
53.0	41.44214	7	7
54.0	42.033827	4	4
55.0	42.619684	4	4
56.0	43.199769	6	6
57.0	43.774139	2	2
58.0	44.34285	1	1
59.0	44.905957	4	4
60.0	45.463517	6	6
61.0	46.015583	7	7
62.0	46.562209	1	1
63.0	47.10345	1	1
64.0	47.639359	7	7
65.0	48.169987	3	3
66.0	48.695387	1	1
67.0	49.215611	2	2
68.0	49.730709	1	1
69.0	50.240732	0	0
70.0	50.74573	4	4
71.0	51.245752	2	2
72.0	51.740848	1	1
73.0	52.231066	3	3
74.0	52.716454	7	7
75.0	53.19706	2	2
76.0	53.67293	2	2
77.0	54.144112	2	2
78.0	54.610652	2	2
79.0	55.072594	2	2
80.0	55.529986	3	3
81.0	55.982871	0	0
82.0	56.431294	2	2
83.0	56.875299	3	3
84.0	57.314929	3	3
85.0	57.750228	3	3
86.0	58.181238	1	1
87.0	58.608001	3	3
88.0	59.030559	0	0
89.0	59.448955	4	4
90.0	59.863228	5	5
91.0	60.273419	0	0
92.0	60.679569	2	2
93.0	61.081717	1	1
94.0	61.479903	5	5
95.0	61.874166	4	4
96.0	62.264544	1	1
97.0	62.651076	1	1
98.0	63.0338	0	0
99.0	63.412753	4	4
100.0	63.787972	3	3
101.0	0	3	3
103.0	0	2	2
105.0	0	2	2
107.0	0	2	2
108.0	0	1	1
109.0	0	1	1
110.0	0	1	1
113.0	0	2	2
116.0	0	1	1
118.0	0	3	3
119.0	0	1	1
123.0	0	2	2
127.0	0	1	1
128.0	0	1	1
130.0	0	1	1
131.0	0	1	1
138.0	0	2	2
140.0	0	1	1
141.0	0	1	1
142.0	0	2	2
146.0	0	1	1
147.0	0	2	2
149.0	0	1	1
152.0	0	1	1
155.0	0	1	1
157.0	0	1	1
158.0	0	1	1
159.0	0	1	1
168.0	0	1	1
173.0	0	1	1
176.0	0	1	1
179.0	0	1	1
186.0	0	1	1
188.0	0	4	4
189.0	0	2	2
192.0	0	1	1
193.0	0	2	2
198.0	0	1	1
199.0	0	1	1
200.0	0	2	2
203.0	0	1	1
208.0	0	1	1
212.0	0	1	1
213.0	0	2	2
216.0	0	1	1
224.0	0	1	1
230.0	0	1	1
232.0	0	1	1
233.0	0	1	1
235.0	0	1	1
238.0	0	1	1
241.0	0	1	1
242.0	0	1	1
247.0	0	1	1
251.0	0	1	1
261.0	0	1	1
268.0	0	1	1
271.0	0	1	1
276.0	0	1	1
285.0	0	1	1
286.0	0	1	1
287.0	0	1	1
299.0	0	1	1
304.0	0	1	1
319.0	0	1	1
322.0	0	1	1
327.0	0	1	1
337.0	0	1	1
342.0	0	1	1
351.0	0	1	1
362.0	0	1	1
365.0	0	1	1
368.0	0	1	1
389.0	0	1	1
399.0	0	1	1
403.0	0	1	1
425.0	0	1	1
432.0	0	1	1
454.0	0	1	1
460.0	0	1	1
485.0	0	1	1
502.0	0	1	1
521.0	0	1	1
523.0	0	1	1
530.0	0	1	1
620.0	0	1	1
665.0	0	1	1
751.0	0	1	1
1007.0	0	1	1
1129.0	0	1	1
1142.0	0	1	1
1323.0	0	1	1
1413.0	0	1	1
1499.0	0	1	1
1661.0	0	1	1
2405.0	0	1	1
10164.0	0	1	1