## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S48M.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S48M.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S48M.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 12:23:18 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	6255641	26874131	32617322	44169005	1218402	1646631	178731	0.07519	233760323

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.006318	23690967	0	23852139
2.0	1.903347	1450132	175960	1305131
3.0	2.702957	77164	1358	62100
4.0	3.415728	5760	17	4777
5.0	4.05109	1379	1	1292
6.0	4.617451	629	0	616
7.0	5.122303	405	0	390
8.0	5.572328	241	0	240
9.0	5.973479	163	0	163
10.0	6.331064	126	0	124
11.0	6.649814	93	0	93
12.0	6.933947	71	0	72
13.0	7.187223	59	0	55
14.0	7.412993	46	0	47
15.0	7.614244	43	0	43
16.0	7.793638	24	0	21
17.0	7.953549	14	0	15
18.0	8.096094	27	0	26
19.0	8.223159	17	0	20
20.0	8.336423	24	0	24
21.0	8.437387	13	0	11
22.0	8.527386	13	0	13
23.0	8.607611	13	0	12
24.0	8.679124	7	0	6
25.0	8.74287	10	0	10
26.0	8.799693	2	0	3
27.0	8.850345	4	0	3
28.0	8.895496	3	0	3
29.0	8.935743	3	0	5
30.0	8.97162	5	0	4
31.0	9.0036	1	0	0
32.0	9.032107	1	0	1
33.0	9.057518	1	0	2
34.0	9.08017	4	0	3
35.0	9.100361	1	0	1
36.0	9.11836	1	0	1
37.0	9.134404	0	0	0
38.0	9.148706	1	0	2
39.0	9.161454	1	0	1
40.0	9.172818	1	0	2
41.0	9.182948	2	0	0
42.0	9.191977	2	0	2
43.0	9.200026	0	0	0
44.0	9.207201	2	0	2
45.0	9.213597	2	0	2
46.0	9.219298	2	0	2
47.0	9.22438	2	0	2
48.0	9.22891	1	0	1
49.0	9.232948	0	0	1
50.0	9.236547	1	0	0
51.0	9.239756	1	0	1
52.0	9.242616	0	0	0
53.0	9.245165	0	0	0
54.0	9.247438	1	0	1
55.0	9.249464	1	0	1
56.0	9.25127	0	0	1
57.0	9.252879	1	0	0
58.0	9.254314	0	0	0
59.0	9.255593	1	0	1
60.0	9.256733	0	0	1
61.0	9.25775	0	0	0
62.0	9.258656	1	0	1
63.0	9.259463	1	0	0
64.0	9.260183	0	0	0
65.0	9.260825	1	0	1
66.0	9.261397	1	0	1
67.0	9.261907	0	0	0
68.0	9.262361	0	0	0
69.0	9.262766	0	0	1
70.0	9.263127	2	0	1
71.0	9.263449	0	0	0
72.0	9.263736	0	0	0
73.0	9.263992	0	0	0
74.0	9.26422	0	0	0
75.0	9.264423	0	0	0
76.0	9.264604	0	0	0
77.0	9.264766	1	0	2
78.0	9.26491	1	0	1
79.0	9.265038	1	0	0
80.0	9.265153	0	0	0
81.0	9.265255	0	0	0
82.0	9.265345	0	0	0
83.0	9.265426	0	0	0
84.0	9.265499	0	0	0
85.0	9.265563	0	0	0
86.0	9.26562	0	0	0
87.0	9.265672	0	0	0
88.0	9.265717	0	0	0
89.0	9.265758	0	0	0
90.0	9.265794	0	0	0
91.0	9.265826	0	0	0
92.0	9.265855	0	0	0
93.0	9.265881	0	0	0
94.0	9.265904	0	0	0
95.0	9.265924	0	0	0
96.0	9.265942	0	0	0
97.0	9.265958	0	0	0
98.0	9.265973	0	0	1
99.0	9.265986	1	0	0
100.0	9.265997	0	0	0
205.0	0	0	0	1
207.0	0	1	0	0
346.0	0	0	0	1
350.0	0	1	0	0