## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/standard/BerglandTeach/mapping_output/ExpEvo_PRJEB5713_CO_4_2014_MM_DD/ExpEvo_PRJEB5713_CO_4_2014_MM_DD.sorted_merged.bam] OUTPUT=/standard/BerglandTeach/mapping_output/ExpEvo_PRJEB5713_CO_4_2014_MM_DD/ExpEvo_PRJEB5713_CO_4_2014_MM_DD.dedup.bam METRICS_FILE=/standard/BerglandTeach/mapping_output/ExpEvo_PRJEB5713_CO_4_2014_MM_DD/ExpEvo_PRJEB5713_CO_4_2014_MM_DD.mark_duplicates_report.txt REMOVE_DUPLICATES=true VALIDATION_STRINGENCY=SILENT    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 COMPRESSION_LEVEL=5 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: Tue Sep 17 16:13:57 UTC 2024

## 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
lib1	3562428	21618444	0	0	736380	7516	0	0.016056	31083607763

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	21531756	21531756
2.0	1.999305	7438	7438
3.0	2.997915	39	39
4.0	3.99583	0	0
5.0	4.993052	0	0
6.0	5.989581	0	0
7.0	6.985417	0	0
8.0	7.98056	0	0
9.0	8.975012	0	0
10.0	9.968772	0	0
11.0	10.961841	0	0
12.0	11.95422	0	0
13.0	12.945908	0	0
14.0	13.936908	0	0
15.0	14.927218	0	0
16.0	15.91684	0	0
17.0	16.905774	0	0
18.0	17.89402	0	0
19.0	18.881579	0	0
20.0	19.868452	0	0
21.0	20.854638	0	0
22.0	21.840139	0	0
23.0	22.824954	0	0
24.0	23.809085	0	0
25.0	24.792532	0	0
26.0	25.775295	0	0
27.0	26.757375	0	0
28.0	27.738772	0	0
29.0	28.719486	0	0
30.0	29.699519	0	0
31.0	30.67887	0	0
32.0	31.657541	0	0
33.0	32.635531	0	0
34.0	33.612841	0	0
35.0	34.589471	0	0
36.0	35.565423	0	0
37.0	36.540696	0	0
38.0	37.515291	0	0
39.0	38.489209	0	0
40.0	39.462449	0	0
41.0	40.435013	0	0
42.0	41.4069	0	0
43.0	42.378112	0	0
44.0	43.348648	0	0
45.0	44.31851	0	0
46.0	45.287698	0	0
47.0	46.256211	0	0
48.0	47.224052	0	0
49.0	48.191219	0	0
50.0	49.157714	0	0
51.0	50.123537	0	0
52.0	51.088689	0	0
53.0	52.053169	0	0
54.0	53.016979	0	0
55.0	53.980119	0	0
56.0	54.942589	0	0
57.0	55.90439	0	0
58.0	56.865523	0	0
59.0	57.825987	0	0
60.0	58.785783	0	0
61.0	59.744912	0	0
62.0	60.703374	0	0
63.0	61.66117	0	0
64.0	62.6183	0	0
65.0	63.574765	0	0
66.0	64.530564	0	0
67.0	65.485699	0	0
68.0	66.44017	0	0
69.0	67.393978	0	0
70.0	68.347122	0	0
71.0	69.299604	0	0
72.0	70.251423	0	0
73.0	71.20258	0	0
74.0	72.153077	0	0
75.0	73.102912	0	0
76.0	74.052087	0	0
77.0	75.000602	0	0
78.0	75.948458	0	0
79.0	76.895655	0	0
80.0	77.842193	0	0
81.0	78.788073	0	0
82.0	79.733296	0	0
83.0	80.677861	0	0
84.0	81.62177	0	0
85.0	82.565022	0	0
86.0	83.507618	0	0
87.0	84.44956	0	0
88.0	85.390846	0	0
89.0	86.331478	0	0
90.0	87.271456	0	0
91.0	88.21078	0	0
92.0	89.149451	0	0
93.0	90.08747	0	0
94.0	91.024837	0	0
95.0	91.961551	0	0
96.0	92.897615	0	0
97.0	93.833028	0	0
98.0	94.76779	0	0
99.0	95.701903	0	0
100.0	96.635366	0	0