## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Lvi_Dro_1_2016-09-12/UA_Lvi_Dro_1_2016-09-12.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Lvi_Dro_1_2016-09-12/UA_Lvi_Dro_1_2016-09-12.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Lvi_Dro_1_2016-09-12/UA_Lvi_Dro_1_2016-09-12.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 17:07:05 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	37450710	5238623	0	0	8406041	278835	0	0.187025	47448258

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	4636236	4636236
2.0	1.89547	199607	199607
3.0	2.697335	13184	13184
4.0	3.415382	1698	1698
5.0	4.05837	691	691
6.0	4.634147	440	440
7.0	5.149737	312	312
8.0	5.611433	251	251
9.0	6.024867	199	199
10.0	6.395085	136	136
11.0	6.726604	124	124
12.0	7.023469	105	105
13.0	7.289303	80	80
14.0	7.527349	79	79
15.0	7.740511	59	59
16.0	7.931392	56	56
17.0	8.10232	54	54
18.0	8.255381	49	49
19.0	8.392442	29	29
20.0	8.515176	25	25
21.0	8.625081	27	27
22.0	8.723497	34	34
23.0	8.811626	28	28
24.0	8.890543	21	21
25.0	8.961211	18	18
26.0	9.024491	11	11
27.0	9.081157	17	17
28.0	9.131899	13	13
29.0	9.177338	14	14
30.0	9.218027	7	7
31.0	9.254462	11	11
32.0	9.287089	15	15
33.0	9.316305	14	14
34.0	9.342468	16	16
35.0	9.365895	5	5
36.0	9.386874	11	11
37.0	9.40566	5	5
38.0	9.422482	6	6
39.0	9.437546	3	3
40.0	9.451035	5	5
41.0	9.463114	6	6
42.0	9.47393	5	5
43.0	9.483616	6	6
44.0	9.492289	5	5
45.0	9.500056	7	7
46.0	9.507011	5	5
47.0	9.513239	4	4
48.0	9.518815	7	7
49.0	9.523809	6	6
50.0	9.528281	4	4
51.0	9.532286	4	4
52.0	9.535871	3	3
53.0	9.539082	8	8
54.0	9.541958	5	5
55.0	9.544533	3	3
56.0	9.546838	6	6
57.0	9.548903	2	2
58.0	9.550752	6	6
59.0	9.552407	5	5
60.0	9.55389	4	4
61.0	9.555217	4	4
62.0	9.556406	2	2
63.0	9.557471	4	4
64.0	9.558424	3	3
65.0	9.559278	1	1
66.0	9.560042	3	3
67.0	9.560726	4	4
68.0	9.561339	1	1
69.0	9.561888	2	2
70.0	9.56238	0	0
71.0	9.56282	2	2
72.0	9.563214	0	0
73.0	9.563567	0	0
74.0	9.563883	1	1
75.0	9.564166	4	4
76.0	9.564419	2	2
77.0	9.564646	1	1
78.0	9.564849	3	3
79.0	9.565031	2	2
80.0	9.565194	2	2
81.0	9.56534	0	0
82.0	9.565471	3	3
83.0	9.565588	1	1
84.0	9.565692	0	0
85.0	9.565786	1	1
86.0	9.56587	2	2
87.0	9.565946	2	2
88.0	9.566013	2	2
89.0	9.566073	1	1
90.0	9.566127	0	0
91.0	9.566176	0	0
92.0	9.566219	0	0
93.0	9.566258	0	0
94.0	9.566292	0	0
95.0	9.566324	0	0
96.0	9.566351	2	2
97.0	9.566376	1	1
98.0	9.566399	0	0
99.0	9.566419	0	0
100.0	9.566437	3	3
102.0	0	1	1
105.0	0	1	1
106.0	0	2	2
108.0	0	2	2
109.0	0	1	1
113.0	0	1	1
114.0	0	1	1
116.0	0	1	1
118.0	0	1	1
122.0	0	1	1
124.0	0	1	1
125.0	0	2	2
127.0	0	2	2
133.0	0	1	1
141.0	0	1	1
144.0	0	1	1
145.0	0	1	1
146.0	0	1	1
152.0	0	1	1
155.0	0	1	1
170.0	0	1	1
181.0	0	1	1
188.0	0	1	1
203.0	0	1	1
206.0	0	1	1
211.0	0	1	1
243.0	0	1	1
248.0	0	1	1
250.0	0	1	1
260.0	0	1	1
267.0	0	1	1
284.0	0	1	1
304.0	0	2	2
345.0	0	1	1
447.0	0	1	1
467.0	0	1	1
496.0	0	1	1
605.0	0	1	1
606.0	0	1	1
1570.0	0	1	1