## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Var_1_2014-08-18/UA_Che_Var_1_2014-08-18.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Var_1_2014-08-18/UA_Che_Var_1_2014-08-18.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/UA_Che_Var_1_2014-08-18/UA_Che_Var_1_2014-08-18.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 08:46:06 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	8908448	19751018	0	0	1955361	763607	0	0.071938	248807223

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	18142454	18142454
2.0	1.923686	402992	402992
3.0	2.776883	8053	8053
4.0	3.564968	1065	1065
5.0	4.292912	581	581
6.0	4.965304	415	415
7.0	5.586383	298	298
8.0	6.160065	245	245
9.0	6.689968	201	201
10.0	7.179431	157	157
11.0	7.631542	131	131
12.0	8.04915	131	131
13.0	8.434889	90	90
14.0	8.791191	100	100
15.0	9.120303	83	83
16.0	9.424298	106	106
17.0	9.705095	79	79
18.0	9.964463	73	73
19.0	10.204037	60	60
20.0	10.425329	61	61
21.0	10.629733	52	52
22.0	10.818538	60	60
23.0	10.992935	40	40
24.0	11.154023	53	53
25.0	11.302818	41	41
26.0	11.440257	41	41
27.0	11.567209	27	27
28.0	11.684472	44	44
29.0	11.792786	38	38
30.0	11.892834	34	34
31.0	11.985247	37	37
32.0	12.070608	46	46
33.0	12.149455	20	20
34.0	12.222285	22	22
35.0	12.289556	34	34
36.0	12.351694	29	29
37.0	12.40909	26	26
38.0	12.462106	21	21
39.0	12.511076	29	29
40.0	12.556309	20	20
41.0	12.59809	31	31
42.0	12.636683	24	24
43.0	12.67233	20	20
44.0	12.705257	10	10
45.0	12.735671	15	15
46.0	12.763765	20	20
47.0	12.789714	16	16
48.0	12.813683	11	11
49.0	12.835823	12	12
50.0	12.856273	20	20
51.0	12.875163	16	16
52.0	12.892611	11	11
53.0	12.908727	12	12
54.0	12.923614	19	19
55.0	12.937365	16	16
56.0	12.950066	13	13
57.0	12.961798	15	15
58.0	12.972635	7	7
59.0	12.982644	16	16
60.0	12.99189	15	15
61.0	13.00043	12	12
62.0	13.008319	6	6
63.0	13.015605	5	5
64.0	13.022336	7	7
65.0	13.028552	15	15
66.0	13.034295	11	11
67.0	13.039599	11	11
68.0	13.044498	8	8
69.0	13.049024	16	16
70.0	13.053204	8	8
71.0	13.057065	11	11
72.0	13.060632	8	8
73.0	13.063926	8	8
74.0	13.066969	10	10
75.0	13.069779	8	8
76.0	13.072376	10	10
77.0	13.074774	5	5
78.0	13.076989	5	5
79.0	13.079035	8	8
80.0	13.080925	7	7
81.0	13.08267	7	7
82.0	13.084283	7	7
83.0	13.085772	11	11
84.0	13.087148	12	12
85.0	13.088419	12	12
86.0	13.089592	5	5
87.0	13.090676	11	11
88.0	13.091678	8	8
89.0	13.092603	11	11
90.0	13.093457	9	9
91.0	13.094247	5	5
92.0	13.094976	5	5
93.0	13.095649	7	7
94.0	13.096271	7	7
95.0	13.096845	6	6
96.0	13.097376	4	4
97.0	13.097866	5	5
98.0	13.098319	5	5
99.0	13.098737	10	10
100.0	13.099124	11	11
101.0	0	8	8
102.0	0	9	9
103.0	0	5	5
104.0	0	5	5
105.0	0	6	6
106.0	0	5	5
107.0	0	4	4
108.0	0	7	7
109.0	0	5	5
110.0	0	1	1
111.0	0	5	5
112.0	0	8	8
113.0	0	8	8
114.0	0	4	4
115.0	0	4	4
116.0	0	4	4
117.0	0	1	1
118.0	0	9	9
119.0	0	4	4
120.0	0	2	2
121.0	0	4	4
122.0	0	3	3
123.0	0	6	6
124.0	0	7	7
125.0	0	6	6
126.0	0	3	3
127.0	0	4	4
128.0	0	6	6
129.0	0	4	4
131.0	0	3	3
132.0	0	6	6
133.0	0	3	3
134.0	0	5	5
135.0	0	3	3
136.0	0	5	5
137.0	0	6	6
138.0	0	3	3
139.0	0	3	3
140.0	0	4	4
141.0	0	4	4
142.0	0	9	9
143.0	0	2	2
144.0	0	4	4
145.0	0	4	4
146.0	0	5	5
147.0	0	2	2
148.0	0	3	3
149.0	0	1	1
150.0	0	3	3
151.0	0	7	7
152.0	0	2	2
153.0	0	1	1
154.0	0	2	2
155.0	0	4	4
157.0	0	4	4
158.0	0	2	2
160.0	0	6	6
161.0	0	5	5
162.0	0	2	2
163.0	0	6	6
165.0	0	2	2
166.0	0	6	6
167.0	0	2	2
168.0	0	3	3
169.0	0	3	3
170.0	0	4	4
171.0	0	4	4
172.0	0	2	2
173.0	0	3	3
174.0	0	1	1
175.0	0	2	2
176.0	0	1	1
177.0	0	2	2
178.0	0	2	2
179.0	0	1	1
180.0	0	1	1
182.0	0	2	2
183.0	0	4	4
184.0	0	4	4
185.0	0	2	2
186.0	0	3	3
187.0	0	1	1
189.0	0	3	3
190.0	0	3	3
191.0	0	3	3
192.0	0	1	1
193.0	0	1	1
194.0	0	2	2
195.0	0	4	4
196.0	0	4	4
197.0	0	2	2
198.0	0	4	4
199.0	0	1	1
200.0	0	1	1
201.0	0	3	3
202.0	0	3	3
203.0	0	1	1
204.0	0	2	2
205.0	0	3	3
206.0	0	2	2
207.0	0	3	3
208.0	0	4	4
211.0	0	1	1
212.0	0	1	1
213.0	0	1	1
215.0	0	3	3
216.0	0	1	1
218.0	0	2	2
219.0	0	3	3
220.0	0	1	1
223.0	0	3	3
224.0	0	3	3
226.0	0	1	1
227.0	0	2	2
228.0	0	2	2
230.0	0	1	1
231.0	0	3	3
232.0	0	2	2
233.0	0	2	2
234.0	0	1	1
235.0	0	2	2
239.0	0	2	2
242.0	0	1	1
245.0	0	2	2
246.0	0	1	1
248.0	0	3	3
249.0	0	1	1
250.0	0	1	1
252.0	0	1	1
253.0	0	1	1
254.0	0	1	1
255.0	0	1	1
256.0	0	3	3
257.0	0	1	1
259.0	0	2	2
260.0	0	1	1
262.0	0	1	1
263.0	0	1	1
264.0	0	1	1
265.0	0	1	1
266.0	0	1	1
267.0	0	1	1
268.0	0	2	2
269.0	0	3	3
270.0	0	1	1
271.0	0	1	1
272.0	0	1	1
275.0	0	2	2
276.0	0	1	1
277.0	0	1	1
278.0	0	2	2
279.0	0	1	1
280.0	0	2	2
281.0	0	1	1
282.0	0	1	1
284.0	0	3	3
285.0	0	4	4
286.0	0	1	1
288.0	0	2	2
289.0	0	4	4
290.0	0	2	2
291.0	0	2	2
292.0	0	3	3
293.0	0	1	1
295.0	0	3	3
296.0	0	3	3
298.0	0	2	2
299.0	0	1	1
300.0	0	1	1
301.0	0	2	2
302.0	0	1	1
305.0	0	3	3
309.0	0	2	2
311.0	0	2	2
312.0	0	3	3
314.0	0	1	1
315.0	0	2	2
317.0	0	1	1
319.0	0	1	1
320.0	0	1	1
321.0	0	2	2
323.0	0	1	1
326.0	0	1	1
328.0	0	3	3
330.0	0	2	2
334.0	0	1	1
336.0	0	2	2
337.0	0	1	1
338.0	0	1	1
339.0	0	1	1
345.0	0	2	2
346.0	0	1	1
347.0	0	1	1
348.0	0	1	1
349.0	0	1	1
350.0	0	3	3
352.0	0	1	1
357.0	0	1	1
358.0	0	1	1
360.0	0	2	2
363.0	0	2	2
366.0	0	1	1
368.0	0	1	1
369.0	0	1	1
372.0	0	1	1
375.0	0	1	1
376.0	0	1	1
378.0	0	1	1
382.0	0	1	1
385.0	0	1	1
386.0	0	1	1
388.0	0	1	1
390.0	0	1	1
392.0	0	1	1
398.0	0	1	1
400.0	0	1	1
405.0	0	1	1
407.0	0	5	5
409.0	0	1	1
411.0	0	2	2
412.0	0	1	1
413.0	0	1	1
414.0	0	1	1
419.0	0	2	2
421.0	0	1	1
422.0	0	1	1
426.0	0	3	3
427.0	0	2	2
432.0	0	1	1
434.0	0	1	1
435.0	0	1	1
436.0	0	1	1
439.0	0	1	1
442.0	0	1	1
445.0	0	1	1
451.0	0	2	2
454.0	0	1	1
457.0	0	1	1
460.0	0	2	2
461.0	0	1	1
464.0	0	2	2
465.0	0	1	1
468.0	0	1	1
469.0	0	1	1
470.0	0	3	3
471.0	0	1	1
475.0	0	1	1
476.0	0	1	1
481.0	0	1	1
482.0	0	2	2
483.0	0	1	1
485.0	0	1	1
492.0	0	2	2
493.0	0	3	3
494.0	0	1	1
495.0	0	1	1
499.0	0	1	1
500.0	0	1	1
508.0	0	1	1
510.0	0	2	2
511.0	0	1	1
518.0	0	1	1
523.0	0	1	1
524.0	0	1	1
527.0	0	1	1
528.0	0	2	2
531.0	0	1	1
538.0	0	1	1
540.0	0	3	3
541.0	0	1	1
549.0	0	3	3
550.0	0	1	1
553.0	0	1	1
562.0	0	1	1
563.0	0	1	1
564.0	0	1	1
566.0	0	1	1
575.0	0	1	1
579.0	0	2	2
580.0	0	1	1
583.0	0	1	1
595.0	0	1	1
598.0	0	3	3
601.0	0	1	1
606.0	0	2	2
617.0	0	1	1
618.0	0	1	1
622.0	0	2	2
627.0	0	1	1
629.0	0	1	1
631.0	0	1	1
632.0	0	1	1
633.0	0	1	1
635.0	0	1	1
646.0	0	1	1
647.0	0	1	1
652.0	0	1	1
656.0	0	1	1
657.0	0	1	1
660.0	0	1	1
661.0	0	2	2
669.0	0	1	1
670.0	0	1	1
677.0	0	1	1
679.0	0	2	2
682.0	0	1	1
683.0	0	1	1
688.0	0	1	1
692.0	0	1	1
695.0	0	1	1
696.0	0	1	1
699.0	0	1	1
705.0	0	1	1
708.0	0	1	1
713.0	0	1	1
719.0	0	1	1
723.0	0	1	1
728.0	0	2	2
729.0	0	1	1
738.0	0	1	1
740.0	0	1	1
744.0	0	1	1
746.0	0	1	1
772.0	0	1	1
780.0	0	1	1
781.0	0	1	1
787.0	0	1	1
790.0	0	1	1
804.0	0	1	1
815.0	0	1	1
818.0	0	1	1
820.0	0	2	2
829.0	0	1	1
839.0	0	1	1
840.0	0	1	1
845.0	0	1	1
851.0	0	2	2
855.0	0	1	1
875.0	0	1	1
910.0	0	2	2
928.0	0	1	1
935.0	0	1	1
940.0	0	1	1
941.0	0	1	1
951.0	0	1	1
953.0	0	1	1
959.0	0	1	1
962.0	0	1	1
964.0	0	1	1
967.0	0	1	1
977.0	0	1	1
988.0	0	1	1
995.0	0	1	1
998.0	0	1	1
1012.0	0	1	1
1017.0	0	1	1
1021.0	0	1	1
1041.0	0	1	1
1058.0	0	1	1
1062.0	0	1	1
1069.0	0	1	1
1072.0	0	2	2
1114.0	0	1	1
1117.0	0	1	1
1139.0	0	1	1
1169.0	0	1	1
1179.0	0	1	1
1187.0	0	1	1
1193.0	0	1	1
1207.0	0	1	1
1232.0	0	1	1
1247.0	0	1	1
1248.0	0	1	1
1256.0	0	1	1
1265.0	0	1	1
1272.0	0	1	1
1290.0	0	1	1
1395.0	0	1	1
1446.0	0	1	1
1471.0	0	1	1
1481.0	0	1	1
1486.0	0	1	1
1603.0	0	1	1
1619.0	0	1	1
1626.0	0	1	1
1633.0	0	1	1
1857.0	0	1	1
2104.0	0	1	1