## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Tuo_1_2013-12-08/US_Cal_Tuo_1_2013-12-08.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Tuo_1_2013-12-08/US_Cal_Tuo_1_2013-12-08.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/US_Cal_Tuo_1_2013-12-08/US_Cal_Tuo_1_2013-12-08.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 17:39:38 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	1582675	29624869	0	0	463819	1733139	0	0.064605	243217344

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	26238284	26238284
2.0	1.885322	1097088	1097088
3.0	2.669116	42142	42142
4.0	3.363027	3655	3655
5.0	3.977361	1382	1382
6.0	4.521244	965	965
7.0	5.002756	646	646
8.0	5.429049	480	480
9.0	5.806455	396	396
10.0	6.140581	283	283
11.0	6.436391	253	253
12.0	6.698277	210	210
13.0	6.93013	180	180
14.0	7.135395	173	173
15.0	7.317121	137	137
16.0	7.478007	114	114
17.0	7.620442	122	122
18.0	7.746544	99	99
19.0	7.858184	115	115
20.0	7.957021	86	86
21.0	8.044524	85	85
22.0	8.121993	73	73
23.0	8.190577	64	64
24.0	8.251296	65	65
25.0	8.305052	75	75
26.0	8.352644	58	58
27.0	8.394778	39	39
28.0	8.43208	53	53
29.0	8.465104	51	51
30.0	8.494341	51	51
31.0	8.520225	48	48
32.0	8.543141	42	42
33.0	8.563429	37	37
34.0	8.58139	39	39
35.0	8.597292	43	43
36.0	8.61137	30	30
37.0	8.623833	24	24
38.0	8.634867	26	26
39.0	8.644636	30	30
40.0	8.653285	40	40
41.0	8.660942	30	30
42.0	8.66772	28	28
43.0	8.673722	28	28
44.0	8.679035	31	31
45.0	8.683739	24	24
46.0	8.687903	23	23
47.0	8.69159	22	22
48.0	8.694854	23	23
49.0	8.697744	12	12
50.0	8.700302	19	19
51.0	8.702567	20	20
52.0	8.704572	25	25
53.0	8.706347	18	18
54.0	8.707919	17	17
55.0	8.70931	12	12
56.0	8.710542	14	14
57.0	8.711633	23	23
58.0	8.712598	12	12
59.0	8.713453	10	10
60.0	8.71421	24	24
61.0	8.71488	17	17
62.0	8.715473	17	17
63.0	8.715998	17	17
64.0	8.716463	13	13
65.0	8.716875	16	16
66.0	8.717239	12	12
67.0	8.717562	9	9
68.0	8.717847	12	12
69.0	8.7181	15	15
70.0	8.718324	6	6
71.0	8.718522	13	13
72.0	8.718698	13	13
73.0	8.718853	7	7
74.0	8.718991	13	13
75.0	8.719112	7	7
76.0	8.71922	13	13
77.0	8.719316	9	9
78.0	8.7194	5	5
79.0	8.719475	10	10
80.0	8.719541	14	14
81.0	8.7196	8	8
82.0	8.719652	10	10
83.0	8.719698	8	8
84.0	8.719738	8	8
85.0	8.719774	7	7
86.0	8.719806	4	4
87.0	8.719834	7	7
88.0	8.719859	7	7
89.0	8.719881	11	11
90.0	8.719901	6	6
91.0	8.719918	7	7
92.0	8.719934	10	10
93.0	8.719947	6	6
94.0	8.719959	3	3
95.0	8.71997	6	6
96.0	8.719979	7	7
97.0	8.719988	6	6
98.0	8.719995	6	6
99.0	8.720002	7	7
100.0	8.720008	9	9
101.0	0	6	6
102.0	0	9	9
103.0	0	4	4
104.0	0	6	6
105.0	0	4	4
106.0	0	7	7
107.0	0	2	2
108.0	0	8	8
109.0	0	4	4
110.0	0	7	7
111.0	0	4	4
112.0	0	4	4
113.0	0	10	10
114.0	0	8	8
115.0	0	4	4
116.0	0	7	7
117.0	0	9	9
118.0	0	7	7
119.0	0	6	6
120.0	0	3	3
121.0	0	4	4
122.0	0	4	4
123.0	0	7	7
124.0	0	5	5
125.0	0	5	5
126.0	0	8	8
127.0	0	4	4
128.0	0	5	5
129.0	0	3	3
130.0	0	7	7
131.0	0	2	2
132.0	0	2	2
133.0	0	3	3
134.0	0	9	9
136.0	0	2	2
137.0	0	2	2
138.0	0	6	6
139.0	0	5	5
140.0	0	6	6
141.0	0	3	3
142.0	0	2	2
143.0	0	5	5
144.0	0	5	5
145.0	0	5	5
146.0	0	3	3
147.0	0	4	4
148.0	0	2	2
150.0	0	7	7
151.0	0	5	5
152.0	0	4	4
153.0	0	1	1
154.0	0	5	5
155.0	0	3	3
156.0	0	1	1
158.0	0	2	2
160.0	0	1	1
161.0	0	2	2
162.0	0	4	4
163.0	0	5	5
164.0	0	1	1
165.0	0	1	1
166.0	0	1	1
167.0	0	6	6
168.0	0	4	4
169.0	0	3	3
170.0	0	7	7
171.0	0	4	4
172.0	0	4	4
173.0	0	3	3
174.0	0	6	6
175.0	0	2	2
176.0	0	3	3
177.0	0	4	4
178.0	0	6	6
179.0	0	3	3
180.0	0	1	1
181.0	0	6	6
182.0	0	1	1
183.0	0	2	2
184.0	0	4	4
185.0	0	2	2
186.0	0	4	4
187.0	0	2	2
188.0	0	3	3
189.0	0	5	5
190.0	0	3	3
191.0	0	5	5
192.0	0	6	6
193.0	0	7	7
194.0	0	4	4
195.0	0	3	3
196.0	0	3	3
197.0	0	3	3
198.0	0	2	2
199.0	0	2	2
200.0	0	3	3
201.0	0	5	5
202.0	0	1	1
203.0	0	3	3
204.0	0	6	6
205.0	0	3	3
206.0	0	1	1
207.0	0	2	2
209.0	0	3	3
210.0	0	2	2
211.0	0	1	1
212.0	0	2	2
213.0	0	2	2
214.0	0	2	2
215.0	0	4	4
216.0	0	2	2
217.0	0	2	2
218.0	0	2	2
219.0	0	3	3
220.0	0	1	1
221.0	0	2	2
222.0	0	3	3
223.0	0	2	2
224.0	0	1	1
225.0	0	2	2
226.0	0	3	3
227.0	0	4	4
228.0	0	2	2
229.0	0	3	3
230.0	0	3	3
231.0	0	2	2
232.0	0	7	7
233.0	0	1	1
234.0	0	2	2
235.0	0	2	2
236.0	0	5	5
237.0	0	4	4
238.0	0	3	3
239.0	0	3	3
240.0	0	4	4
242.0	0	2	2
243.0	0	2	2
244.0	0	2	2
245.0	0	2	2
246.0	0	3	3
247.0	0	2	2
248.0	0	3	3
249.0	0	4	4
250.0	0	2	2
251.0	0	2	2
252.0	0	2	2
254.0	0	3	3
255.0	0	2	2
256.0	0	2	2
257.0	0	2	2
258.0	0	2	2
259.0	0	2	2
260.0	0	2	2
261.0	0	3	3
262.0	0	1	1
263.0	0	2	2
264.0	0	3	3
265.0	0	1	1
266.0	0	1	1
267.0	0	3	3
268.0	0	2	2
269.0	0	1	1
270.0	0	1	1
271.0	0	1	1
272.0	0	1	1
273.0	0	3	3
275.0	0	1	1
276.0	0	2	2
277.0	0	2	2
278.0	0	2	2
279.0	0	2	2
280.0	0	2	2
281.0	0	2	2
282.0	0	4	4
283.0	0	3	3
284.0	0	3	3
285.0	0	2	2
286.0	0	2	2
288.0	0	3	3
289.0	0	2	2
290.0	0	1	1
291.0	0	3	3
292.0	0	1	1
293.0	0	3	3
295.0	0	3	3
296.0	0	1	1
297.0	0	1	1
298.0	0	1	1
299.0	0	3	3
300.0	0	2	2
301.0	0	4	4
302.0	0	1	1
303.0	0	1	1
305.0	0	2	2
306.0	0	4	4
307.0	0	4	4
308.0	0	2	2
309.0	0	4	4
310.0	0	2	2
311.0	0	2	2
312.0	0	1	1
313.0	0	1	1
316.0	0	2	2
317.0	0	1	1
320.0	0	1	1
321.0	0	2	2
323.0	0	1	1
324.0	0	1	1
325.0	0	2	2
326.0	0	1	1
327.0	0	1	1
328.0	0	1	1
330.0	0	2	2
331.0	0	1	1
332.0	0	4	4
334.0	0	3	3
335.0	0	2	2
340.0	0	2	2
343.0	0	2	2
344.0	0	1	1
347.0	0	1	1
348.0	0	3	3
349.0	0	1	1
350.0	0	2	2
351.0	0	1	1
353.0	0	1	1
354.0	0	2	2
355.0	0	3	3
357.0	0	3	3
358.0	0	1	1
360.0	0	2	2
361.0	0	2	2
362.0	0	1	1
363.0	0	1	1
364.0	0	2	2
365.0	0	3	3
368.0	0	1	1
370.0	0	1	1
371.0	0	1	1
372.0	0	2	2
374.0	0	3	3
375.0	0	2	2
378.0	0	2	2
379.0	0	1	1
382.0	0	1	1
384.0	0	3	3
385.0	0	2	2
387.0	0	1	1
388.0	0	2	2
389.0	0	1	1
390.0	0	2	2
391.0	0	3	3
393.0	0	1	1
394.0	0	1	1
395.0	0	2	2
397.0	0	2	2
399.0	0	1	1
400.0	0	2	2
404.0	0	1	1
406.0	0	1	1
407.0	0	1	1
409.0	0	1	1
410.0	0	1	1
411.0	0	4	4
413.0	0	1	1
418.0	0	2	2
420.0	0	1	1
423.0	0	2	2
425.0	0	2	2
426.0	0	1	1
427.0	0	1	1
428.0	0	1	1
429.0	0	2	2
431.0	0	1	1
432.0	0	1	1
433.0	0	1	1
434.0	0	1	1
435.0	0	1	1
436.0	0	1	1
438.0	0	1	1
439.0	0	1	1
441.0	0	1	1
442.0	0	1	1
443.0	0	3	3
444.0	0	1	1
447.0	0	1	1
448.0	0	1	1
449.0	0	2	2
453.0	0	1	1
454.0	0	1	1
456.0	0	1	1
458.0	0	1	1
459.0	0	1	1
460.0	0	1	1
463.0	0	1	1
464.0	0	1	1
466.0	0	1	1
470.0	0	1	1
471.0	0	1	1
474.0	0	1	1
476.0	0	1	1
478.0	0	3	3
479.0	0	1	1
480.0	0	3	3
481.0	0	1	1
482.0	0	1	1
484.0	0	1	1
487.0	0	2	2
491.0	0	1	1
492.0	0	1	1
495.0	0	1	1
496.0	0	1	1
497.0	0	1	1
498.0	0	1	1
500.0	0	2	2
501.0	0	1	1
503.0	0	1	1
504.0	0	1	1
506.0	0	1	1
507.0	0	1	1
508.0	0	1	1
509.0	0	1	1
522.0	0	1	1
523.0	0	2	2
526.0	0	1	1
528.0	0	2	2
532.0	0	1	1
533.0	0	1	1
534.0	0	1	1
535.0	0	1	1
537.0	0	3	3
538.0	0	2	2
543.0	0	1	1
548.0	0	1	1
551.0	0	1	1
553.0	0	1	1
555.0	0	2	2
557.0	0	1	1
567.0	0	1	1
568.0	0	1	1
570.0	0	1	1
572.0	0	1	1
573.0	0	1	1
575.0	0	1	1
576.0	0	1	1
577.0	0	1	1
578.0	0	1	1
584.0	0	1	1
585.0	0	1	1
587.0	0	1	1
589.0	0	1	1
591.0	0	1	1
592.0	0	1	1
601.0	0	1	1
602.0	0	1	1
603.0	0	1	1
604.0	0	1	1
608.0	0	2	2
609.0	0	1	1
611.0	0	1	1
613.0	0	1	1
615.0	0	1	1
617.0	0	1	1
620.0	0	2	2
623.0	0	1	1
624.0	0	1	1
627.0	0	2	2
630.0	0	2	2
631.0	0	1	1
632.0	0	1	1
633.0	0	1	1
636.0	0	1	1
641.0	0	1	1
643.0	0	1	1
646.0	0	1	1
649.0	0	1	1
654.0	0	1	1
656.0	0	1	1
660.0	0	1	1
669.0	0	1	1
674.0	0	1	1
675.0	0	1	1
681.0	0	1	1
689.0	0	1	1
691.0	0	1	1
697.0	0	2	2
701.0	0	2	2
702.0	0	1	1
703.0	0	1	1
705.0	0	1	1
708.0	0	1	1
709.0	0	1	1
710.0	0	1	1
713.0	0	2	2
723.0	0	1	1
725.0	0	1	1
726.0	0	1	1
727.0	0	1	1
729.0	0	1	1
736.0	0	1	1
739.0	0	2	2
743.0	0	1	1
744.0	0	1	1
749.0	0	3	3
751.0	0	1	1
752.0	0	1	1
754.0	0	1	1
755.0	0	1	1
759.0	0	1	1
766.0	0	1	1
767.0	0	1	1
769.0	0	1	1
774.0	0	1	1
776.0	0	1	1
781.0	0	1	1
782.0	0	1	1
785.0	0	2	2
797.0	0	1	1
798.0	0	1	1
802.0	0	1	1
803.0	0	1	1
813.0	0	1	1
815.0	0	1	1
816.0	0	1	1
817.0	0	1	1
818.0	0	1	1
824.0	0	1	1
825.0	0	1	1
827.0	0	1	1
842.0	0	1	1
849.0	0	1	1
853.0	0	2	2
868.0	0	1	1
872.0	0	1	1
879.0	0	1	1
880.0	0	1	1
883.0	0	1	1
888.0	0	1	1
889.0	0	1	1
895.0	0	1	1
897.0	0	1	1
900.0	0	1	1
905.0	0	1	1
908.0	0	1	1
911.0	0	1	1
931.0	0	1	1
940.0	0	1	1
950.0	0	1	1
953.0	0	1	1
960.0	0	2	2
975.0	0	1	1
982.0	0	1	1
985.0	0	1	1
988.0	0	1	1
990.0	0	1	1
993.0	0	1	1
999.0	0	1	1
1002.0	0	1	1
1013.0	0	1	1
1024.0	0	1	1
1036.0	0	1	1
1061.0	0	1	1
1063.0	0	1	1
1070.0	0	1	1
1071.0	0	1	1
1084.0	0	2	2
1089.0	0	1	1
1092.0	0	1	1
1100.0	0	1	1
1123.0	0	1	1
1126.0	0	1	1
1128.0	0	1	1
1130.0	0	1	1
1170.0	0	1	1
1175.0	0	1	1
1177.0	0	1	1
1181.0	0	2	2
1185.0	0	1	1
1188.0	0	1	1
1200.0	0	1	1
1217.0	0	1	1
1218.0	0	1	1
1232.0	0	1	1
1235.0	0	1	1
1238.0	0	1	1
1264.0	0	2	2
1289.0	0	1	1
1291.0	0	2	2
1294.0	0	1	1
1300.0	0	1	1
1324.0	0	1	1
1342.0	0	1	1
1343.0	0	1	1
1388.0	0	1	1
1417.0	0	1	1
1468.0	0	1	1
1486.0	0	1	1
1497.0	0	1	1
1503.0	0	1	1
1518.0	0	1	1
1624.0	0	1	1
1649.0	0	1	1
1673.0	0	1	1
1675.0	0	1	1
1776.0	0	1	1
1784.0	0	1	1
1810.0	0	1	1
1883.0	0	1	1
2105.0	0	1	1
2108.0	0	1	1
2157.0	0	1	1
2194.0	0	1	1
2365.0	0	1	1
2381.0	0	1	1
2456.0	0	1	1
2527.0	0	1	1
2684.0	0	1	1
2787.0	0	1	1
2813.0	0	1	1
3084.0	0	1	1
3442.0	0	1	1
3554.0	0	1	1
3729.0	0	1	1
4345.0	0	1	1
4550.0	0	1	1