## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S13M.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S13M.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S13M.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 11:18:17 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	2584013	11782397	15121632	18595063	429341	555189	46147	0.058883	131351889

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.003758	10722771	0	10765171
2.0	1.921399	474682	45656	435670
3.0	2.76031	23664	242	20494
4.0	3.527246	3027	1	2855
5.0	4.228382	1081	1	1051
6.0	4.869364	584	0	580
7.0	5.455353	356	0	352
8.0	5.991066	242	0	238
9.0	6.480818	151	0	153
10.0	6.928551	101	0	101
11.0	7.337871	87	0	82
12.0	7.712073	60	0	64
13.0	8.05417	56	0	53
14.0	8.366916	49	0	49
15.0	8.652831	36	0	37
16.0	8.914215	40	0	39
17.0	9.153174	21	0	19
18.0	9.371631	14	0	17
19.0	9.571345	19	0	18
20.0	9.753925	18	0	16
21.0	9.92084	13	0	13
22.0	10.073435	12	0	12
23.0	10.212938	12	0	12
24.0	10.340472	13	0	13
25.0	10.457064	4	0	6
26.0	10.563653	7	0	6
27.0	10.661097	12	0	11
28.0	10.750181	9	0	11
29.0	10.831622	7	0	5
30.0	10.906076	1	0	2
31.0	10.974142	5	0	4
32.0	11.036368	7	0	9
33.0	11.093255	6	0	4
34.0	11.145262	3	0	3
35.0	11.192807	0	0	0
36.0	11.236272	1	0	1
37.0	11.276009	3	0	3
38.0	11.312336	2	0	2
39.0	11.345547	1	0	1
40.0	11.375908	1	0	1
41.0	11.403664	2	0	2
42.0	11.429039	0	0	0
43.0	11.452237	2	0	2
44.0	11.473445	1	0	1
45.0	11.492833	2	0	3
46.0	11.510558	2	0	1
47.0	11.526762	1	0	1
48.0	11.541576	2	0	2
49.0	11.555119	2	0	2
50.0	11.5675	0	0	0
51.0	11.578818	2	0	2
52.0	11.589166	0	0	0
53.0	11.598626	1	0	1
54.0	11.607274	1	0	1
55.0	11.61518	1	0	1
56.0	11.622408	0	0	0
57.0	11.629016	0	0	0
58.0	11.635057	0	0	0
59.0	11.640579	0	0	0
60.0	11.645628	0	0	0
61.0	11.650244	0	0	0
62.0	11.654463	1	0	1
63.0	11.658321	0	0	0
64.0	11.661848	0	0	0
65.0	11.665072	0	0	0
66.0	11.668019	0	0	0
67.0	11.670714	0	0	0
68.0	11.673177	0	0	0
69.0	11.675429	0	0	0
70.0	11.677488	0	0	0
71.0	11.67937	0	0	0
72.0	11.681091	0	0	0
73.0	11.682664	0	0	0
74.0	11.684102	0	0	0
75.0	11.685417	0	0	0
76.0	11.686619	0	0	0
77.0	11.687717	0	0	0
78.0	11.688722	0	0	0
79.0	11.68964	0	0	0
80.0	11.69048	0	0	0
81.0	11.691247	0	0	0
82.0	11.691949	0	0	0
83.0	11.692591	0	0	0
84.0	11.693177	0	0	0
85.0	11.693713	0	0	0
86.0	11.694203	0	0	0
87.0	11.694651	1	0	1
88.0	11.695061	0	0	0
89.0	11.695436	0	0	0
90.0	11.695778	0	0	0
91.0	11.696091	1	0	1
92.0	11.696377	0	0	0
93.0	11.696639	0	0	0
94.0	11.696878	0	0	0
95.0	11.697096	0	0	0
96.0	11.697296	0	0	0
97.0	11.697479	0	0	0
98.0	11.697646	0	0	0
99.0	11.697799	0	0	0
100.0	11.697938	0	0	0
109.0	0	0	0	1
110.0	0	1	0	0
130.0	0	0	0	1
131.0	0	1	0	0
132.0	0	1	0	1
174.0	0	0	0	1
175.0	0	1	0	0
183.0	0	0	0	1
186.0	0	1	0	0
199.0	0	0	0	1
201.0	0	1	0	0
220.0	0	0	0	1
222.0	0	1	0	0
358.0	0	0	0	1
362.0	0	1	0	0