## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/standard/BerglandTeach/mapping_output/ExpEvo_PRJEB5713_VSP_1_2014_MM_DD/ExpEvo_PRJEB5713_VSP_1_2014_MM_DD.sorted_merged.bam] OUTPUT=/standard/BerglandTeach/mapping_output/ExpEvo_PRJEB5713_VSP_1_2014_MM_DD/ExpEvo_PRJEB5713_VSP_1_2014_MM_DD.dedup.bam METRICS_FILE=/standard/BerglandTeach/mapping_output/ExpEvo_PRJEB5713_VSP_1_2014_MM_DD/ExpEvo_PRJEB5713_VSP_1_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: Sat Sep 14 20:22:34 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	3563234	26717372	0	0	839089	8880	0	0.015033	40183546795

## HISTOGRAM	java.lang.Double
BIN	VALUE	all_sets	non_optical_sets
1.0	1	26611271	26611271
2.0	1.999335	8801	8801
3.0	2.998006	38	38
4.0	3.996014	1	1
5.0	4.993358	0	0
6.0	5.990039	0	0
7.0	6.986058	0	0
8.0	7.981414	0	0
9.0	8.976109	0	0
10.0	9.970143	0	0
11.0	10.963516	0	0
12.0	11.956229	0	0
13.0	12.948282	0	0
14.0	13.939676	0	0
15.0	14.930411	0	0
16.0	15.920487	0	0
17.0	16.909906	0	0
18.0	17.898666	0	0
19.0	18.88677	0	0
20.0	19.874216	0	0
21.0	20.861007	0	0
22.0	21.847141	0	0
23.0	22.83262	0	0
24.0	23.817444	0	0
25.0	24.801614	0	0
26.0	25.785129	0	0
27.0	26.767991	0	0
28.0	27.750199	0	0
29.0	28.731754	0	0
30.0	29.712657	0	0
31.0	30.692909	0	0
32.0	31.672508	0	0
33.0	32.651457	0	0
34.0	33.629754	0	0
35.0	34.607402	0	0
36.0	35.5844	0	0
37.0	36.560748	0	0
38.0	37.536448	0	0
39.0	38.511499	0	0
40.0	39.485901	0	0
41.0	40.459657	0	0
42.0	41.432765	0	0
43.0	42.405226	0	0
44.0	43.377041	0	0
45.0	44.34821	0	0
46.0	45.318733	0	0
47.0	46.288611	0	0
48.0	47.257845	0	0
49.0	48.226434	0	0
50.0	49.19438	0	0
51.0	50.161683	0	0
52.0	51.128342	0	0
53.0	52.094359	0	0
54.0	53.059734	0	0
55.0	54.024467	0	0
56.0	54.988559	0	0
57.0	55.95201	0	0
58.0	56.914821	0	0
59.0	57.876992	0	0
60.0	58.838523	0	0
61.0	59.799415	0	0
62.0	60.759669	0	0
63.0	61.719284	0	0
64.0	62.678262	0	0
65.0	63.636602	0	0
66.0	64.594305	0	0
67.0	65.551372	0	0
68.0	66.507802	0	0
69.0	67.463597	0	0
70.0	68.418756	0	0
71.0	69.373281	0	0
72.0	70.327171	0	0
73.0	71.280427	0	0
74.0	72.23305	0	0
75.0	73.185039	0	0
76.0	74.136396	0	0
77.0	75.08712	0	0
78.0	76.037213	0	0
79.0	76.986674	0	0
80.0	77.935503	0	0
81.0	78.883703	0	0
82.0	79.831272	0	0
83.0	80.778211	0	0
84.0	81.724521	0	0
85.0	82.670201	0	0
86.0	83.615254	0	0
87.0	84.559678	0	0
88.0	85.503474	0	0
89.0	86.446643	0	0
90.0	87.389185	0	0
91.0	88.331101	0	0
92.0	89.272391	0	0
93.0	90.213055	0	0
94.0	91.153093	0	0
95.0	92.092507	0	0
96.0	93.031297	0	0
97.0	93.969462	0	0
98.0	94.907005	0	0
99.0	95.843923	0	0
100.0	96.78022	0	0