## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/project/berglandlab/DEST/dest_mapped/DESTv1/PT_Por_Rec_1_2016-10-01/PT_Por_Rec_1_2016-10-01.sorted_merged.bam] OUTPUT=/project/berglandlab/DEST/dest_mapped/DESTv1/PT_Por_Rec_1_2016-10-01/PT_Por_Rec_1_2016-10-01.dedup.bam METRICS_FILE=/project/berglandlab/DEST/dest_mapped/DESTv1/PT_Por_Rec_1_2016-10-01/PT_Por_Rec_1_2016-10-01.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 09:46:26 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	41022014	18819981	0	0	10467003	1542549	0	0.172283	108444283

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	15627674	15627674
2.0	1.840679	1137667	1137667
3.0	2.547421	91923	91923
4.0	3.141564	9865	9865
5.0	3.641047	2413	2413
6.0	4.060952	1290	1290
7.0	4.413958	821	821
8.0	4.710723	640	640
9.0	4.960207	526	526
10.0	5.169942	362	362
11.0	5.346263	294	294
12.0	5.494492	256	256
13.0	5.619105	206	206
14.0	5.723865	165	165
15.0	5.811934	147	147
16.0	5.885972	145	145
17.0	5.948214	143	143
18.0	6.00054	147	147
19.0	6.044529	111	111
20.0	6.081509	113	113
21.0	6.112598	92	92
22.0	6.138734	102	102
23.0	6.160706	120	120
24.0	6.179177	104	104
25.0	6.194706	76	76
26.0	6.20776	94	94
27.0	6.218735	82	82
28.0	6.227961	64	64
29.0	6.235717	68	68
30.0	6.242237	59	59
31.0	6.247719	72	72
32.0	6.252327	51	51
33.0	6.256201	43	43
34.0	6.259458	51	51
35.0	6.262196	45	45
36.0	6.264498	36	36
37.0	6.266433	43	43
38.0	6.26806	36	36
39.0	6.269427	30	30
40.0	6.270577	38	38
41.0	6.271544	34	34
42.0	6.272356	30	30
43.0	6.273039	21	21
44.0	6.273613	24	24
45.0	6.274096	31	31
46.0	6.274502	24	24
47.0	6.274843	13	13
48.0	6.27513	19	19
49.0	6.275371	24	24
50.0	6.275574	15	15
51.0	6.275744	23	23
52.0	6.275888	12	12
53.0	6.276008	12	12
54.0	6.276109	14	14
55.0	6.276194	16	16
56.0	6.276266	6	6
57.0	6.276326	13	13
58.0	6.276377	17	17
59.0	6.276419	20	20
60.0	6.276455	23	23
61.0	6.276485	8	8
62.0	6.27651	13	13
63.0	6.276532	15	15
64.0	6.276549	13	13
65.0	6.276564	10	10
66.0	6.276577	11	11
67.0	6.276588	10	10
68.0	6.276597	9	9
69.0	6.276604	15	15
70.0	6.27661	13	13
71.0	6.276616	11	11
72.0	6.27662	9	9
73.0	6.276624	14	14
74.0	6.276627	10	10
75.0	6.27663	15	15
76.0	6.276632	18	18
77.0	6.276634	11	11
78.0	6.276635	13	13
79.0	6.276637	9	9
80.0	6.276638	10	10
81.0	6.276639	7	7
82.0	6.276639	16	16
83.0	6.27664	12	12
84.0	6.276641	11	11
85.0	6.276641	13	13
86.0	6.276642	14	14
87.0	6.276642	13	13
88.0	6.276642	8	8
89.0	6.276642	10	10
90.0	6.276643	5	5
91.0	6.276643	11	11
92.0	6.276643	11	11
93.0	6.276643	3	3
94.0	6.276643	14	14
95.0	6.276643	9	9
96.0	6.276643	6	6
97.0	6.276643	6	6
98.0	6.276643	8	8
99.0	6.276643	6	6
100.0	6.276643	5	5
101.0	0	3	3
102.0	0	2	2
103.0	0	8	8
104.0	0	2	2
105.0	0	5	5
106.0	0	9	9
107.0	0	4	4
108.0	0	1	1
109.0	0	6	6
110.0	0	6	6
111.0	0	4	4
112.0	0	8	8
113.0	0	3	3
114.0	0	3	3
115.0	0	3	3
116.0	0	6	6
117.0	0	5	5
118.0	0	4	4
119.0	0	4	4
120.0	0	4	4
121.0	0	7	7
122.0	0	1	1
123.0	0	3	3
124.0	0	4	4
125.0	0	2	2
126.0	0	2	2
127.0	0	2	2
128.0	0	1	1
129.0	0	3	3
130.0	0	2	2
131.0	0	4	4
132.0	0	4	4
133.0	0	1	1
135.0	0	3	3
136.0	0	1	1
137.0	0	5	5
138.0	0	1	1
139.0	0	2	2
140.0	0	1	1
141.0	0	4	4
142.0	0	4	4
143.0	0	1	1
144.0	0	2	2
145.0	0	1	1
146.0	0	2	2
147.0	0	2	2
149.0	0	1	1
151.0	0	3	3
152.0	0	3	3
153.0	0	3	3
154.0	0	1	1
155.0	0	1	1
157.0	0	1	1
158.0	0	3	3
160.0	0	2	2
161.0	0	1	1
163.0	0	3	3
164.0	0	1	1
165.0	0	1	1
166.0	0	2	2
167.0	0	2	2
168.0	0	1	1
169.0	0	1	1
171.0	0	1	1
175.0	0	1	1
176.0	0	1	1
178.0	0	1	1
179.0	0	5	5
180.0	0	1	1
181.0	0	1	1
182.0	0	2	2
183.0	0	2	2
184.0	0	1	1
186.0	0	1	1
188.0	0	2	2
189.0	0	1	1
190.0	0	1	1
191.0	0	1	1
195.0	0	1	1
200.0	0	2	2
204.0	0	3	3
206.0	0	1	1
219.0	0	1	1
220.0	0	1	1
221.0	0	1	1
222.0	0	2	2
223.0	0	1	1
224.0	0	1	1
234.0	0	1	1
239.0	0	1	1
245.0	0	1	1
253.0	0	2	2
254.0	0	1	1
256.0	0	1	1
257.0	0	1	1
260.0	0	1	1
261.0	0	1	1
262.0	0	1	1
263.0	0	2	2
264.0	0	1	1
266.0	0	1	1
269.0	0	2	2
271.0	0	1	1
274.0	0	1	1
275.0	0	1	1
276.0	0	1	1
279.0	0	2	2
282.0	0	1	1
283.0	0	1	1
291.0	0	1	1
300.0	0	1	1
308.0	0	2	2
312.0	0	1	1
314.0	0	1	1
323.0	0	2	2
336.0	0	1	1
343.0	0	3	3
344.0	0	1	1
347.0	0	1	1
367.0	0	1	1
370.0	0	1	1
395.0	0	2	2
396.0	0	1	1
403.0	0	1	1
447.0	0	1	1
506.0	0	1	1
514.0	0	1	1
533.0	0	1	1
698.0	0	1	1
1057.0	0	1	1