## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1209_23/G1209_23_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1209_23/G1209_23_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workjul/Alignment/2025-03-28_Rogachev/G1209_23/G1209_23_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	35874	60098306	62784358	44890	3405	1129719	0	0.018821	1578445763

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	1	57862450	57862450
2.0	1.962641	1083273	1083273
3.0	2.88932	22201	22201
4.0	3.781379	616	616
5.0	4.640112	41	41
6.0	5.466763	4	4
7.0	6.262532	2	2
8.0	7.028573	0	0
9.0	7.765995	0	0
10.0	8.475868	0	0
11.0	9.159221	0	0
12.0	9.817045	0	0
13.0	10.450293	0	0
14.0	11.059885	0	0
15.0	11.646702	0	0
16.0	12.211597	0	0
17.0	12.755389	0	0
18.0	13.278865	0	0
19.0	13.782784	0	0
20.0	14.267878	0	0
21.0	14.73485	0	0
22.0	15.184376	0	0
23.0	15.617108	0	0
24.0	16.033674	0	0
25.0	16.434678	0	0
26.0	16.820701	0	0
27.0	17.192302	0	0
28.0	17.550021	0	0
29.0	17.894376	0	0
30.0	18.225867	0	0
31.0	18.544973	0	0
32.0	18.852158	0	0
33.0	19.147867	0	0
34.0	19.432529	0	0
35.0	19.706556	0	0
36.0	19.970346	0	0
37.0	20.224281	0	0
38.0	20.468729	0	0
39.0	20.704046	0	0
40.0	20.930571	0	0
41.0	21.148633	0	0
42.0	21.358549	0	0
43.0	21.560622	0	0
44.0	21.755147	0	0
45.0	21.942404	0	0
46.0	22.122666	0	0
47.0	22.296193	0	0
48.0	22.463238	0	0
49.0	22.624042	0	0
50.0	22.778838	0	0
51.0	22.927852	0	0
52.0	23.071298	0	0
53.0	23.209386	0	0
54.0	23.342315	0	0
55.0	23.470278	0	0
56.0	23.59346	0	0
57.0	23.712041	0	0
58.0	23.826191	0	0
59.0	23.936077	0	0
60.0	24.041858	0	0
61.0	24.143687	0	0
62.0	24.241711	0	0
63.0	24.336074	0	0
64.0	24.426911	0	0
65.0	24.514355	0	0
66.0	24.598532	0	0
67.0	24.679564	0	0
68.0	24.757569	0	0
69.0	24.83266	0	0
70.0	24.904946	0	0
71.0	24.974531	0	0
72.0	25.041516	0	0
73.0	25.105999	0	0
74.0	25.168073	0	0
75.0	25.227828	0	0
76.0	25.285351	0	0
77.0	25.340725	0	0
78.0	25.39403	0	0
79.0	25.445343	0	0
80.0	25.49474	0	0
81.0	25.542291	0	0
82.0	25.588066	0	0
83.0	25.632131	0	0
84.0	25.674549	0	0
85.0	25.715383	0	0
86.0	25.754691	0	0
87.0	25.792531	0	0
88.0	25.828957	0	0
89.0	25.864022	0	0
90.0	25.897778	0	0
91.0	25.930272	0	0
92.0	25.961552	0	0
93.0	25.991664	0	0
94.0	26.020651	0	0
95.0	26.048554	0	0
96.0	26.075416	0	0
97.0	26.101274	0	0
98.0	26.126166	0	0
99.0	26.150128	0	0
100.0	26.173195	0	0