## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S6M.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S6M.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S6M.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 13:04:59 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	3953129	17855415	19699953	28939727	584237	759118	74565	0.053007	224957628

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.004029	16378586	0	16447832
2.0	1.931447	687834	73753	623553
3.0	2.788099	26320	403	21624
4.0	3.579385	1942	2	1699
5.0	4.310293	525	0	507
6.0	4.985429	274	0	275
7.0	5.60905	205	0	199
8.0	6.185086	124	0	124
9.0	6.717168	81	0	83
10.0	7.20865	85	0	82
11.0	7.66263	38	0	40
12.0	8.08197	42	0	38
13.0	8.469312	42	0	42
14.0	8.827098	24	0	24
15.0	9.157584	21	0	26
16.0	9.462852	24	0	19
17.0	9.744827	15	0	16
18.0	10.005287	11	0	10
19.0	10.245872	7	0	9
20.0	10.468099	14	0	12
21.0	10.67337	6	0	7
22.0	10.862978	10	0	10
23.0	11.038118	6	0	6
24.0	11.199894	3	0	2
25.0	11.349325	4	0	5
26.0	11.487355	2	0	1
27.0	11.614852	6	0	6
28.0	11.732621	2	0	3
29.0	11.841404	4	0	3
30.0	11.941886	2	0	3
31.0	12.0347	7	0	7
32.0	12.120433	4	0	3
33.0	12.199624	1	0	2
34.0	12.272772	3	0	2
35.0	12.340339	0	0	0
36.0	12.40275	1	0	1
37.0	12.460399	1	0	1
38.0	12.513649	4	0	4
39.0	12.562836	1	0	1
40.0	12.60827	1	0	2
41.0	12.650237	1	0	2
42.0	12.689002	2	0	1
43.0	12.724808	2	0	1
44.0	12.757883	1	0	1
45.0	12.788434	0	0	0
46.0	12.816654	0	0	0
47.0	12.84272	0	0	0
48.0	12.866798	1	0	2
49.0	12.889038	1	0	1
50.0	12.909581	2	0	1
51.0	12.928557	0	0	0
52.0	12.946084	0	0	0
53.0	12.962275	0	0	0
54.0	12.97723	0	0	0
55.0	12.991044	0	0	0
56.0	13.003803	0	0	0
57.0	13.01559	2	0	2
58.0	13.026476	0	0	0
59.0	13.036532	0	0	0
60.0	13.045821	0	0	0
61.0	13.054401	0	0	0
62.0	13.062327	0	0	0
63.0	13.069647	0	0	0
64.0	13.076409	0	0	0
65.0	13.082655	0	0	0
66.0	13.088425	0	0	0
67.0	13.093754	0	0	0
68.0	13.098676	0	0	0
69.0	13.103223	0	0	0
70.0	13.107423	0	0	0
71.0	13.111303	0	0	0
72.0	13.114886	0	0	0
73.0	13.118196	0	0	0
74.0	13.121254	0	0	0
75.0	13.124078	0	0	0
76.0	13.126687	0	0	0
77.0	13.129096	0	0	0
78.0	13.131322	0	0	0
79.0	13.133378	0	0	0
80.0	13.135277	0	0	0
81.0	13.137031	0	0	0
82.0	13.138652	0	0	0
83.0	13.140148	0	0	0
84.0	13.141531	0	0	0
85.0	13.142808	0	0	0
86.0	13.143987	0	0	0
87.0	13.145077	0	0	0
88.0	13.146083	0	0	0
89.0	13.147013	0	0	1
90.0	13.147872	1	0	1
91.0	13.148665	1	0	0
92.0	13.149397	0	0	0
93.0	13.150074	0	0	0
94.0	13.150699	0	0	0
95.0	13.151277	0	0	0
96.0	13.15181	0	0	0
97.0	13.152303	0	0	0
98.0	13.152758	0	0	0
99.0	13.153178	0	0	0
100.0	13.153566	0	0	0
155.0	0	0	0	1
156.0	0	1	0	0