## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[S12M.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S12M.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S12M.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 11:11:23 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	3671993	15654415	18592978	25235299	500715	722750	69010	0.055637	180548639

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	optical_sets	non_optical_sets
1.0	1.004239	14260545	0	14324418
2.0	1.925073	639018	68360	579857
3.0	2.76943	27087	319	22645
4.0	3.543662	2367	4	2132
5.0	4.253592	791	0	779
6.0	4.90456	475	0	467
7.0	5.501465	288	0	283
8.0	6.048795	213	0	213
9.0	6.550668	138	0	132
10.0	7.01086	108	0	111
11.0	7.432831	101	0	100
12.0	7.819757	66	0	64
13.0	8.174548	64	0	66
14.0	8.499873	53	0	48
15.0	8.798179	42	0	43
16.0	9.07171	37	0	38
17.0	9.322523	36	0	34
18.0	9.552506	22	0	23
19.0	9.763388	24	0	23
20.0	9.956757	21	0	22
21.0	10.134065	17	0	16
22.0	10.296648	10	0	10
23.0	10.445727	16	0	16
24.0	10.582426	8	0	7
25.0	10.707771	9	0	9
26.0	10.822706	4	0	5
27.0	10.928096	7	0	6
28.0	11.024732	6	0	7
29.0	11.113343	8	0	9
30.0	11.194595	6	0	4
31.0	11.269098	7	0	8
32.0	11.337414	5	0	5
33.0	11.400056	8	0	8
34.0	11.457495	7	0	8
35.0	11.510164	5	0	3
36.0	11.558458	2	0	2
37.0	11.602742	3	0	4
38.0	11.643348	3	0	3
39.0	11.680581	2	0	4
40.0	11.714722	5	0	2
41.0	11.746028	0	0	0
42.0	11.774734	1	0	2
43.0	11.801055	3	0	2
44.0	11.825191	4	0	4
45.0	11.847322	0	0	0
46.0	11.867615	1	0	1
47.0	11.886222	1	0	1
48.0	11.903284	1	0	1
49.0	11.91893	1	0	2
50.0	11.933275	1	0	0
51.0	11.94643	0	0	1
52.0	11.958491	1	0	0
53.0	11.969551	1	0	3
54.0	11.979693	3	0	1
55.0	11.988992	1	0	1
56.0	11.997519	0	0	0
57.0	12.005338	1	0	1
58.0	12.012507	0	0	0
59.0	12.019081	0	0	0
60.0	12.025109	0	0	0
61.0	12.030636	1	0	1
62.0	12.035705	0	0	0
63.0	12.040352	0	0	0
64.0	12.044613	1	0	1
65.0	12.048521	0	0	0
66.0	12.052104	0	0	0
67.0	12.055389	0	0	0
68.0	12.058402	0	0	0
69.0	12.061164	0	0	0
70.0	12.063697	1	0	1
71.0	12.066019	1	0	1
72.0	12.068149	0	0	0
73.0	12.070102	0	0	0
74.0	12.071892	0	0	0
75.0	12.073534	1	0	1
76.0	12.07504	0	0	0
77.0	12.07642	0	0	0
78.0	12.077686	2	0	2
79.0	12.078847	0	0	0
80.0	12.079911	0	0	0
81.0	12.080887	0	0	0
82.0	12.081782	0	0	0
83.0	12.082602	1	0	1
84.0	12.083355	0	0	1
85.0	12.084045	1	0	0
86.0	12.084677	0	0	0
87.0	12.085257	0	0	0
88.0	12.085789	0	0	0
89.0	12.086277	1	0	1
90.0	12.086724	0	0	0
91.0	12.087134	1	0	1
92.0	12.08751	0	0	0
93.0	12.087855	0	0	0
94.0	12.088171	0	0	0
95.0	12.088461	0	0	0
96.0	12.088727	0	0	0
97.0	12.088971	0	0	0
98.0	12.089194	0	0	0
99.0	12.089399	0	0	0
100.0	12.089587	0	0	0