## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S7M.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S7M.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S7M.dup_metrics.txt REMOVE_DUPLICATES=true    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 VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 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: Wed Mar 09 13:23:20 PST 2022

## 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
Unknown Library	3054568	13485124	16838036	21087920	388564	606880	52755	0.053367	158295968

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.003763	12346379	0	12395280
2.0	1.925556	501024	52202	455526
3.0	2.772075	22388	273	19182
4.0	3.549465	3156	1	3001
5.0	4.263373	1442	1	1434
6.0	4.918982	881	0	862
7.0	5.521052	570	0	566
8.0	6.073957	396	0	395
9.0	6.581711	322	0	325
10.0	7.048	239	0	235
11.0	7.476212	195	0	194
12.0	7.869455	143	0	140
13.0	8.230586	120	0	122
14.0	8.562226	108	0	106
15.0	8.866783	88	0	90
16.0	9.14647	67	0	63
17.0	9.403318	57	0	59
18.0	9.63919	73	0	71
19.0	9.855801	64	0	65
20.0	10.054724	37	0	36
21.0	10.237402	37	0	38
22.0	10.405162	31	0	32
23.0	10.559222	38	0	38
24.0	10.700702	29	0	24
25.0	10.830628	23	0	24
26.0	10.949945	20	0	22
27.0	11.059517	23	0	24
28.0	11.160142	23	0	20
29.0	11.25255	15	0	16
30.0	11.337412	16	0	16
31.0	11.415343	11	0	9
32.0	11.486911	16	0	17
33.0	11.552634	14	0	13
34.0	11.61299	16	0	17
35.0	11.668418	5	0	7
36.0	11.719319	14	0	14
37.0	11.766063	8	0	7
38.0	11.80899	14	0	12
39.0	11.848412	7	0	7
40.0	11.884615	7	0	9
41.0	11.917861	11	0	9
42.0	11.948392	6	0	8
43.0	11.97643	6	0	4
44.0	12.002178	8	0	8
45.0	12.025824	7	0	8
46.0	12.047539	5	0	5
47.0	12.06748	4	0	3
48.0	12.085793	2	0	3
49.0	12.102611	6	0	5
50.0	12.118055	2	0	2
51.0	12.132238	3	0	3
52.0	12.145263	2	0	2
53.0	12.157224	2	0	3
54.0	12.168208	2	0	2
55.0	12.178296	2	0	3
56.0	12.187559	4	0	4
57.0	12.196067	5	0	4
58.0	12.203879	1	0	0
59.0	12.211054	1	0	1
60.0	12.217642	1	0	2
61.0	12.223693	2	0	1
62.0	12.229249	4	0	5
63.0	12.234352	2	0	1
64.0	12.239038	3	0	3
65.0	12.243341	2	0	2
66.0	12.247293	0	0	0
67.0	12.250923	0	0	0
68.0	12.254255	3	0	3
69.0	12.257316	2	0	2
70.0	12.260127	0	0	0
71.0	12.262708	1	0	1
72.0	12.265078	2	0	2
73.0	12.267255	0	0	0
74.0	12.269254	0	0	0
75.0	12.27109	0	0	1
76.0	12.272776	1	0	1
77.0	12.274324	1	0	0
78.0	12.275746	1	0	1
79.0	12.277052	0	0	0
80.0	12.278251	1	0	1
81.0	12.279352	0	0	0
82.0	12.280363	0	0	0
83.0	12.281292	1	0	1
84.0	12.282145	1	0	1
85.0	12.282928	0	0	0
86.0	12.283647	0	0	0
87.0	12.284308	0	0	0
88.0	12.284914	1	0	1
89.0	12.285471	0	0	0
90.0	12.285983	1	0	1
91.0	12.286453	0	0	0
92.0	12.286884	0	0	1
93.0	12.28728	1	0	0
94.0	12.287644	0	0	0
95.0	12.287978	0	0	0
96.0	12.288285	0	0	0
97.0	12.288567	0	0	0
98.0	12.288825	0	0	0
99.0	12.289063	0	0	0
100.0	12.289281	0	0	0
102.0	0	1	0	1
105.0	0	0	0	1
106.0	0	2	0	1
108.0	0	0	0	1
109.0	0	1	0	1
111.0	0	2	0	2
112.0	0	1	0	0
114.0	0	4	0	4
117.0	0	1	0	2
119.0	0	1	0	0
127.0	0	0	0	1
128.0	0	1	0	0
130.0	0	1	0	1
133.0	0	0	0	1
134.0	0	1	0	0
169.0	0	0	0	1
170.0	0	1	0	0
238.0	0	0	0	1
242.0	0	1	0	0