## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1084_22/G1084_22_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1084_22/G1084_22_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1084_22/G1084_22_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 15:41:04 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	23200	36415556	33575319	32336	2107	1038137	0	0.028528	626491602

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	34374587	34374587
2.0	1.943531	969240	969240
3.0	2.833781	32109	32109
4.0	3.67376	1329	1329
5.0	4.466306	108	108
6.0	5.214098	31	31
7.0	5.919663	7	7
8.0	6.585385	5	5
9.0	7.213514	1	1
10.0	7.806173	0	0
11.0	8.365366	2	2
12.0	8.892981	0	0
13.0	9.390802	0	0
14.0	9.860512	0	0
15.0	10.303698	0	0
16.0	10.721857	0	0
17.0	11.116404	0	0
18.0	11.48867	0	0
19.0	11.839915	0	0
20.0	12.171326	0	0
21.0	12.484022	0	0
22.0	12.779061	0	0
23.0	13.057438	0	0
24.0	13.320097	0	0
25.0	13.567923	0	0
26.0	13.801754	0	0
27.0	14.022382	0	0
28.0	14.23055	0	0
29.0	14.426964	0	0
30.0	14.612286	0	0
31.0	14.787143	0	0
32.0	14.952127	0	0
33.0	15.107794	0	0
34.0	15.25467	0	0
35.0	15.393252	0	0
36.0	15.524009	0	0
37.0	15.647382	0	0
38.0	15.763789	0	0
39.0	15.873622	0	0
40.0	15.977253	0	0
41.0	16.075031	0	0
42.0	16.167289	0	0
43.0	16.254336	0	0
44.0	16.336469	0	0
45.0	16.413963	0	0
46.0	16.487081	0	0
47.0	16.55607	0	0
48.0	16.621164	0	0
49.0	16.682582	0	0
50.0	16.740531	0	0
51.0	16.795209	0	0
52.0	16.846798	0	0
53.0	16.895475	0	0
54.0	16.941402	0	0
55.0	16.984737	0	0
56.0	17.025624	0	0
57.0	17.064202	0	0
58.0	17.100602	0	0
59.0	17.134946	0	0
60.0	17.167351	0	0
61.0	17.197926	0	0
62.0	17.226775	0	0
63.0	17.253994	0	0
64.0	17.279677	0	0
65.0	17.303909	0	0
66.0	17.326773	0	0
67.0	17.348345	0	0
68.0	17.3687	0	0
69.0	17.387905	0	0
70.0	17.406025	0	0
71.0	17.423123	0	0
72.0	17.439255	0	0
73.0	17.454476	0	0
74.0	17.468837	0	0
75.0	17.482387	0	0
76.0	17.495173	0	0
77.0	17.507236	0	0
78.0	17.518618	0	0
79.0	17.529357	0	0
80.0	17.53949	0	0
81.0	17.549051	0	0
82.0	17.558072	0	0
83.0	17.566583	0	0
84.0	17.574614	0	0
85.0	17.582191	0	0
86.0	17.589341	0	0
87.0	17.596086	0	0
88.0	17.602451	0	0
89.0	17.608457	0	0
90.0	17.614123	0	0
91.0	17.619469	0	0
92.0	17.624514	0	0
93.0	17.629273	0	0
94.0	17.633764	0	0
95.0	17.638001	0	0
96.0	17.641999	0	0
97.0	17.645771	0	0
98.0	17.64933	0	0
99.0	17.652688	0	0
100.0	17.655857	0	0