## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1663_21/G1663_21_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1663_21/G1663_21_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1663_21/G1663_21_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 15:41:01 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	11160	6690032	6944457	42344	526	157933	0	0.023627	139455771

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	6380931	6380931
2.0	1.95316	145599	145599
3.0	2.861674	5274	5274
4.0	3.727634	224	224
5.0	4.553031	8	8
6.0	5.339768	5	5
7.0	6.089653	5	5
8.0	6.804414	7	7
9.0	7.485696	0	0
10.0	8.135067	4	4
11.0	8.754021	2	2
12.0	9.343983	4	4
13.0	9.906311	3	3
14.0	10.4423	4	4
15.0	10.953184	3	3
16.0	11.440137	1	1
17.0	11.904282	3	3
18.0	12.346686	3	3
19.0	12.768368	1	1
20.0	13.170299	1	1
21.0	13.553403	0	0
22.0	13.918562	1	1
23.0	14.266618	1	1
24.0	14.59837	1	1
25.0	14.914584	0	0
26.0	15.215986	1	1
27.0	15.50327	0	0
28.0	15.777098	0	0
29.0	16.0381	1	1
30.0	16.286876	0	0
31.0	16.524	1	1
32.0	16.750017	0	0
33.0	16.965447	0	0
34.0	17.170787	1	1
35.0	17.366508	0	0
36.0	17.553062	1	1
37.0	17.730878	0	0
38.0	17.900365	2	2
39.0	18.061913	0	0
40.0	18.215894	0	0
41.0	18.362663	0	0
42.0	18.502557	2	2
43.0	18.635898	2	2
44.0	18.762994	0	0
45.0	18.884137	0	0
46.0	18.999605	0	0
47.0	19.109665	1	1
48.0	19.214569	2	2
49.0	19.31456	0	0
50.0	19.409868	0	0
51.0	19.500711	0	0
52.0	19.587299	0	0
53.0	19.669831	0	0
54.0	19.748497	0	0
55.0	19.823479	0	0
56.0	19.894949	0	0
57.0	19.963071	0	0
58.0	20.028002	0	0
59.0	20.089891	0	0
60.0	20.148882	0	0
61.0	20.20511	0	0
62.0	20.258704	0	0
63.0	20.309788	0	0
64.0	20.358478	0	0
65.0	20.404889	0	0
66.0	20.449125	0	0
67.0	20.491289	0	0
68.0	20.531479	0	0
69.0	20.569786	0	0
70.0	20.606298	0	0
71.0	20.641101	0	0
72.0	20.674273	0	0
73.0	20.705891	0	0
74.0	20.736029	0	0
75.0	20.764755	0	0
76.0	20.792135	0	0
77.0	20.818233	0	0
78.0	20.843108	0	0
79.0	20.866818	0	0
80.0	20.889418	0	0
81.0	20.910959	0	0
82.0	20.931491	0	0
83.0	20.951061	0	0
84.0	20.969715	0	0
85.0	20.987495	0	0
86.0	21.004442	0	0
87.0	21.020595	0	0
88.0	21.035992	0	0
89.0	21.050668	0	0
90.0	21.064656	0	0
91.0	21.077989	0	0
92.0	21.090697	0	0
93.0	21.10281	0	0
94.0	21.114356	0	0
95.0	21.125361	0	0
96.0	21.135851	0	0
97.0	21.145849	0	0
98.0	21.155379	0	0
99.0	21.164462	0	0
100.0	21.17312	0	0