## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Gra_Pur_1_2016-08-30/ES_Gra_Pur_1_2016-08-30.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Gra_Pur_1_2016-08-30/ES_Gra_Pur_1_2016-08-30.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/ES_Gra_Pur_1_2016-08-30/ES_Gra_Pur_1_2016-08-30.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 08:57:51 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	29271755	10558898	0	0	5919643	884500	0	0.152584	59453394

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	8713889	8713889
2.0	1.837278	587296	587296
3.0	2.538311	47560	47560
4.0	3.125271	6069	6069
5.0	3.61672	2004	2004
6.0	4.028198	1114	1114
7.0	4.37272	751	751
8.0	4.661181	554	554
9.0	4.902702	432	432
10.0	5.104923	346	346
11.0	5.274238	278	278
12.0	5.416001	273	273
13.0	5.534697	209	209
14.0	5.634078	172	172
15.0	5.717287	178	178
16.0	5.786956	144	144
17.0	5.845289	134	134
18.0	5.89413	130	130
19.0	5.935023	134	134
20.0	5.969262	125	125
21.0	5.997929	116	116
22.0	6.021932	93	93
23.0	6.042029	87	87
24.0	6.058855	77	77
25.0	6.072944	90	90
26.0	6.08474	79	79
27.0	6.094617	62	62
28.0	6.102886	71	71
29.0	6.10981	74	74
30.0	6.115607	59	59
31.0	6.120461	41	41
32.0	6.124525	47	47
33.0	6.127928	37	37
34.0	6.130777	35	35
35.0	6.133162	38	38
36.0	6.135159	34	34
37.0	6.136832	41	41
38.0	6.138232	27	27
39.0	6.139404	21	21
40.0	6.140386	38	38
41.0	6.141207	22	22
42.0	6.141895	27	27
43.0	6.142472	23	23
44.0	6.142954	31	31
45.0	6.143358	20	20
46.0	6.143696	15	15
47.0	6.143979	15	15
48.0	6.144216	19	19
49.0	6.144415	10	10
50.0	6.144581	19	19
51.0	6.14472	18	18
52.0	6.144837	14	14
53.0	6.144934	16	16
54.0	6.145016	24	24
55.0	6.145084	9	9
56.0	6.145141	19	19
57.0	6.145189	16	16
58.0	6.145229	24	24
59.0	6.145263	11	11
60.0	6.145291	9	9
61.0	6.145315	13	13
62.0	6.145335	20	20
63.0	6.145351	12	12
64.0	6.145365	8	8
65.0	6.145376	8	8
66.0	6.145386	15	15
67.0	6.145394	16	16
68.0	6.145401	17	17
69.0	6.145407	13	13
70.0	6.145412	11	11
71.0	6.145416	14	14
72.0	6.145419	13	13
73.0	6.145422	5	5
74.0	6.145424	15	15
75.0	6.145426	16	16
76.0	6.145428	11	11
77.0	6.145429	12	12
78.0	6.14543	8	8
79.0	6.145431	6	6
80.0	6.145432	9	9
81.0	6.145433	10	10
82.0	6.145433	9	9
83.0	6.145434	8	8
84.0	6.145434	11	11
85.0	6.145434	9	9
86.0	6.145435	7	7
87.0	6.145435	9	9
88.0	6.145435	7	7
89.0	6.145435	7	7
90.0	6.145435	8	8
91.0	6.145435	2	2
92.0	6.145436	6	6
93.0	6.145436	4	4
94.0	6.145436	8	8
95.0	6.145436	8	8
96.0	6.145436	6	6
97.0	6.145436	6	6
98.0	6.145436	6	6
99.0	6.145436	10	10
100.0	6.145436	10	10
101.0	0	9	9
102.0	0	4	4
103.0	0	2	2
104.0	0	5	5
105.0	0	6	6
106.0	0	1	1
107.0	0	4	4
108.0	0	3	3
109.0	0	5	5
110.0	0	6	6
111.0	0	3	3
112.0	0	3	3
113.0	0	3	3
114.0	0	4	4
115.0	0	2	2
116.0	0	3	3
117.0	0	6	6
118.0	0	3	3
119.0	0	3	3
120.0	0	1	1
121.0	0	2	2
122.0	0	4	4
123.0	0	5	5
124.0	0	1	1
125.0	0	4	4
127.0	0	1	1
128.0	0	3	3
130.0	0	2	2
131.0	0	1	1
133.0	0	7	7
134.0	0	3	3
135.0	0	2	2
137.0	0	3	3
138.0	0	4	4
139.0	0	1	1
140.0	0	1	1
142.0	0	2	2
143.0	0	4	4
144.0	0	1	1
145.0	0	3	3
146.0	0	3	3
147.0	0	1	1
148.0	0	3	3
149.0	0	3	3
150.0	0	2	2
151.0	0	1	1
152.0	0	2	2
153.0	0	2	2
156.0	0	1	1
158.0	0	1	1
159.0	0	2	2
161.0	0	1	1
164.0	0	1	1
165.0	0	1	1
167.0	0	1	1
168.0	0	2	2
170.0	0	1	1
171.0	0	1	1
172.0	0	1	1
173.0	0	1	1
174.0	0	2	2
175.0	0	2	2
176.0	0	2	2
181.0	0	1	1
182.0	0	2	2
185.0	0	1	1
186.0	0	2	2
187.0	0	1	1
189.0	0	1	1
190.0	0	2	2
194.0	0	1	1
201.0	0	2	2
205.0	0	1	1
208.0	0	2	2
209.0	0	1	1
210.0	0	2	2
211.0	0	1	1
212.0	0	1	1
214.0	0	1	1
216.0	0	1	1
223.0	0	1	1
226.0	0	1	1
227.0	0	1	1
228.0	0	1	1
231.0	0	2	2
232.0	0	1	1
233.0	0	1	1
235.0	0	1	1
236.0	0	1	1
238.0	0	1	1
239.0	0	2	2
240.0	0	1	1
245.0	0	3	3
246.0	0	1	1
248.0	0	1	1
251.0	0	1	1
255.0	0	1	1
258.0	0	1	1
260.0	0	1	1
262.0	0	2	2
267.0	0	1	1
268.0	0	1	1
275.0	0	1	1
283.0	0	1	1
284.0	0	1	1
285.0	0	1	1
287.0	0	1	1
291.0	0	1	1
298.0	0	1	1
299.0	0	1	1
300.0	0	1	1
309.0	0	2	2
310.0	0	1	1
315.0	0	2	2
318.0	0	1	1
319.0	0	1	1
321.0	0	1	1
329.0	0	1	1
336.0	0	1	1
349.0	0	1	1
350.0	0	2	2
362.0	0	1	1
384.0	0	1	1
412.0	0	1	1
419.0	0	1	1
421.0	0	1	1
427.0	0	1	1
433.0	0	1	1
458.0	0	1	1
459.0	0	1	1
474.0	0	1	1
540.0	0	1	1
561.0	0	1	1
611.0	0	1	1
751.0	0	1	1
797.0	0	1	1
817.0	0	1	1
831.0	0	1	1
1375.0	0	1	1
2144.0	0	1	1