## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1129_20/G1129_20_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1129_20/G1129_20_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1129_20/G1129_20_dedup_metrics.txt CREATE_INDEX=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 FLOW_MODE=false FLOW_QUALITY_SUM_STRATEGY=false USE_END_IN_UNPAIRED_READS=false USE_UNPAIRED_CLIPPED_END=false UNPAIRED_END_UNCERTAINTY=0 FLOW_SKIP_FIRST_N_FLOWS=0 FLOW_Q_IS_KNOWN_END=false FLOW_EFFECTIVE_QUALITY_THRESHOLD=15 ADD_PG_TAG_TO_READS=true REMOVE_DUPLICATES=false 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=5 MAX_RECORDS_IN_RAM=500000 CREATE_MD5_FILE=false GA4GH_CLIENT_SECRETS=client_secrets.json USE_JDK_DEFLATER=false USE_JDK_INFLATER=false
## htsjdk.samtools.metrics.StringHeader
# Started on: Fri Aug 29 15:40:43 NOVT 2025

## 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	50319	61572585	60971993	83963	5331	1574075	0	0.025597	1183644635

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	58470768	58470768
2.0	1.94931	1483261	1483261
3.0	2.850501	42805	42805
4.0	3.70601	1534	1534
5.0	4.518153	116	116
6.0	5.28913	20	20
7.0	6.021026	4	4
8.0	6.715822	2	2
9.0	7.3754	0	0
10.0	8.001543	0	0
11.0	8.595948	0	0
12.0	9.160223	0	0
13.0	9.695894	0	0
14.0	10.204413	0	0
15.0	10.687155	0	0
16.0	11.145427	0	0
17.0	11.58047	0	0
18.0	11.99346	0	0
19.0	12.385516	0	0
20.0	12.757699	0	0
21.0	13.111016	0	0
22.0	13.446423	0	0
23.0	13.764829	0	0
24.0	14.067095	0	0
25.0	14.354039	0	0
26.0	14.626438	0	0
27.0	14.885029	0	0
28.0	15.130513	0	0
29.0	15.363552	0	0
30.0	15.58478	0	0
31.0	15.794793	0	0
32.0	15.994161	0	0
33.0	16.183423	0	0
34.0	16.363091	0	0
35.0	16.533652	0	0
36.0	16.695567	0	0
37.0	16.849275	0	0
38.0	16.995191	0	0
39.0	17.133711	0	0
40.0	17.26521	0	0
41.0	17.390043	0	0
42.0	17.508548	0	0
43.0	17.621046	0	0
44.0	17.727842	0	0
45.0	17.829224	0	0
46.0	17.925467	0	0
47.0	18.016832	0	0
48.0	18.103565	0	0
49.0	18.185902	0	0
50.0	18.264066	0	0
51.0	18.338267	0	0
52.0	18.408707	0	0
53.0	18.475576	0	0
54.0	18.539056	0	0
55.0	18.599318	0	0
56.0	18.656526	0	0
57.0	18.710833	0	0
58.0	18.762388	0	0
59.0	18.811329	0	0
60.0	18.85779	0	0
61.0	18.901896	0	0
62.0	18.943766	0	0
63.0	18.983513	0	0
64.0	19.021246	0	0
65.0	19.057066	0	0
66.0	19.09107	0	0
67.0	19.123351	0	0
68.0	19.153995	0	0
69.0	19.183086	0	0
70.0	19.210703	0	0
71.0	19.236919	0	0
72.0	19.261807	0	0
73.0	19.285433	0	0
74.0	19.307862	0	0
75.0	19.329153	0	0
76.0	19.349366	0	0
77.0	19.368553	0	0
78.0	19.386769	0	0
79.0	19.40406	0	0
80.0	19.420476	0	0
81.0	19.436059	0	0
82.0	19.450852	0	0
83.0	19.464896	0	0
84.0	19.478227	0	0
85.0	19.490883	0	0
86.0	19.502898	0	0
87.0	19.514303	0	0
88.0	19.52513	0	0
89.0	19.535408	0	0
90.0	19.545166	0	0
91.0	19.554429	0	0
92.0	19.563222	0	0
93.0	19.571569	0	0
94.0	19.579494	0	0
95.0	19.587016	0	0
96.0	19.594158	0	0
97.0	19.600937	0	0
98.0	19.607373	0	0
99.0	19.613482	0	0
100.0	19.619282	0	0