## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Bar_Bar_1_2012-07-13/ES_Bar_Bar_1_2012-07-13.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Bar_Bar_1_2012-07-13/ES_Bar_Bar_1_2012-07-13.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Bar_Bar_1_2012-07-13/ES_Bar_Bar_1_2012-07-13.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 07:34:08 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	616723	21087489	0	0	115286	173399	0	0.010798	1275212478

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	20686353	20686353
2.0	1.9836	47444	47444
3.0	2.951068	3081	3081
4.0	3.902669	571	571
5.0	4.838663	249	249
6.0	5.759307	144	144
7.0	6.664851	122	122
8.0	7.555545	111	111
9.0	8.43163	56	56
10.0	9.293347	74	74
11.0	10.140932	38	38
12.0	10.974616	45	45
13.0	11.794627	45	45
14.0	12.60119	26	26
15.0	13.394524	29	29
16.0	14.174847	18	18
17.0	14.942373	10	10
18.0	15.697311	4	4
19.0	16.439868	7	7
20.0	17.170246	6	6
21.0	17.888646	6	6
22.0	18.595264	6	6
23.0	19.290293	6	6
24.0	19.973923	7	7
25.0	20.646341	7	7
26.0	21.307731	7	7
27.0	21.958274	7	7
28.0	22.598148	5	5
29.0	23.227528	5	5
30.0	23.846585	4	4
31.0	24.45549	8	8
32.0	25.054408	3	3
33.0	25.643504	2	2
34.0	26.222938	7	7
35.0	26.79287	4	4
36.0	27.353454	2	2
37.0	27.904844	3	3
38.0	28.447192	0	0
39.0	28.980644	4	4
40.0	29.505348	2	2
41.0	30.021446	4	4
42.0	30.52908	0	0
43.0	31.028389	5	5
44.0	31.519508	4	4
45.0	32.002574	7	7
46.0	32.477716	2	2
47.0	32.945066	1	1
48.0	33.404751	3	3
49.0	33.856898	3	3
50.0	34.301629	2	2
51.0	34.739066	2	2
52.0	35.169328	2	2
53.0	35.592535	1	1
54.0	36.0088	3	3
55.0	36.418239	1	1
56.0	36.820962	1	1
57.0	37.217081	0	0
58.0	37.606703	2	2
59.0	37.989936	1	1
60.0	38.366883	2	2
61.0	38.737647	2	2
62.0	39.102332	1	1
63.0	39.461035	1	1
64.0	39.813855	2	2
65.0	40.160889	4	4
66.0	40.502231	3	3
67.0	40.837976	2	2
68.0	41.168213	2	2
69.0	41.493035	0	0
70.0	41.81253	3	3
71.0	42.126784	0	0
72.0	42.435885	3	3
73.0	42.739916	2	2
74.0	43.038961	7	7
75.0	43.333102	1	1
76.0	43.622419	0	0
77.0	43.90699	3	3
78.0	44.186895	2	2
79.0	44.462209	2	2
80.0	44.733007	1	1
81.0	44.999365	3	3
82.0	45.261354	1	1
83.0	45.519046	0	0
84.0	45.772512	2	2
85.0	46.021821	2	2
86.0	46.267042	2	2
87.0	46.50824	2	2
88.0	46.745483	0	0
89.0	46.978835	1	1
90.0	47.20836	1	1
91.0	47.43412	1	1
92.0	47.656178	1	1
93.0	47.874594	0	0
94.0	48.089428	2	2
95.0	48.300739	0	0
96.0	48.508584	0	0
97.0	48.71302	2	2
98.0	48.914103	0	0
99.0	49.111889	1	1
100.0	49.30643	1	1
101.0	0	1	1
103.0	0	2	2
104.0	0	1	1
106.0	0	1	1
107.0	0	3	3
108.0	0	1	1
110.0	0	1	1
111.0	0	1	1
112.0	0	1	1
114.0	0	2	2
117.0	0	1	1
118.0	0	1	1
119.0	0	1	1
121.0	0	1	1
124.0	0	1	1
126.0	0	1	1
129.0	0	2	2
131.0	0	1	1
132.0	0	1	1
135.0	0	1	1
138.0	0	2	2
139.0	0	1	1
140.0	0	2	2
142.0	0	1	1
149.0	0	1	1
150.0	0	1	1
157.0	0	1	1
160.0	0	2	2
166.0	0	1	1
168.0	0	1	1
174.0	0	1	1
175.0	0	1	1
179.0	0	1	1
187.0	0	1	1
194.0	0	1	1
197.0	0	1	1
201.0	0	1	1
212.0	0	1	1
228.0	0	1	1
235.0	0	1	1
242.0	0	1	1
258.0	0	1	1
259.0	0	1	1
264.0	0	1	1
318.0	0	2	2
335.0	0	1	1
344.0	0	1	1
435.0	0	1	1
440.0	0	1	1
564.0	0	1	1
589.0	0	1	1
630.0	0	1	1
658.0	0	1	1
742.0	0	1	1
813.0	0	1	1
882.0	0	1	1
899.0	0	1	1
938.0	0	1	1
1172.0	0	1	1
1186.0	0	1	1
1467.0	0	1	1
1472.0	0	1	1
1700.0	0	1	1
1738.0	0	1	1
1748.0	0	1	1
2161.0	0	1	1
2489.0	0	1	1
3185.0	0	1	1
3346.0	0	1	1
7367.0	0	1	1
8811.0	0	1	1
10188.0	0	1	1
11236.0	0	1	1
25326.0	0	1	1