## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[/beegfs/scratch/ws/ws1/torgunakov-workmay/Alignment/2026-04-13-MGNC/F20_14/F20_14_paired.sorted.bam] OUTPUT=/beegfs/scratch/ws/ws1/torgunakov-workmay/Alignment/2026-04-13-MGNC/F20_14/F20_14_paired.sorted.markdup.bam METRICS_FILE=/beegfs/scratch/ws/ws1/torgunakov-workmay/Alignment/2026-04-13-MGNC/F20_14/F20_14_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: Sun May 10 04:19:52 NOVT 2026

## 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	163	329213	31558	221	95	185642	0	0.563901	166708

## HISTOGRAM	java.lang.Double
BIN	CoverageMult	all_sets	non_optical_sets
1.0	0.999996	65765	65765
2.0	1.138787	32387	32387
3.0	1.158049	19249	19249
4.0	1.160723	11046	11046
5.0	1.161094	6448	6448
6.0	1.161145	3777	3777
7.0	1.161153	2183	2183
8.0	1.161154	1238	1238
9.0	1.161154	686	686
10.0	1.161154	373	373
11.0	1.161154	208	208
12.0	1.161154	100	100
13.0	1.161154	58	58
14.0	1.161154	23	23
15.0	1.161154	8	8
16.0	1.161154	7	7
17.0	1.161154	2	2
18.0	1.161154	1	1
19.0	1.161154	0	0
20.0	1.161154	1	1
21.0	1.161154	0	0
22.0	1.161154	0	0
23.0	1.161154	0	0
24.0	1.161154	0	0
25.0	1.161154	0	0
26.0	1.161154	0	0
27.0	1.161154	0	0
28.0	1.161154	0	0
29.0	1.161154	0	0
30.0	1.161154	0	0
31.0	1.161154	0	0
32.0	1.161154	0	0
33.0	1.161154	0	0
34.0	1.161154	0	0
35.0	1.161154	0	0
36.0	1.161154	0	0
37.0	1.161154	0	0
38.0	1.161154	0	0
39.0	1.161154	0	0
40.0	1.161154	0	0
41.0	1.161154	0	0
42.0	1.161154	0	0
43.0	1.161154	0	0
44.0	1.161154	0	0
45.0	1.161154	0	0
46.0	1.161154	0	0
47.0	1.161154	0	0
48.0	1.161154	0	0
49.0	1.161154	0	0
50.0	1.161154	0	0
51.0	1.161154	0	0
52.0	1.161154	0	0
53.0	1.161154	0	0
54.0	1.161154	0	0
55.0	1.161154	0	0
56.0	1.161154	0	0
57.0	1.161154	0	0
58.0	1.161154	0	0
59.0	1.161154	0	0
60.0	1.161154	0	0
61.0	1.161154	1	1
62.0	1.161154	0	0
63.0	1.161154	0	0
64.0	1.161154	0	0
65.0	1.161154	0	0
66.0	1.161154	0	0
67.0	1.161154	0	0
68.0	1.161154	0	0
69.0	1.161154	0	0
70.0	1.161154	0	0
71.0	1.161154	0	0
72.0	1.161154	0	0
73.0	1.161154	0	0
74.0	1.161154	0	0
75.0	1.161154	0	0
76.0	1.161154	0	0
77.0	1.161154	0	0
78.0	1.161154	0	0
79.0	1.161154	0	0
80.0	1.161154	0	0
81.0	1.161154	0	0
82.0	1.161154	0	0
83.0	1.161154	0	0
84.0	1.161154	0	0
85.0	1.161154	0	0
86.0	1.161154	0	0
87.0	1.161154	0	0
88.0	1.161154	0	0
89.0	1.161154	0	0
90.0	1.161154	0	0
91.0	1.161154	0	0
92.0	1.161154	0	0
93.0	1.161154	0	0
94.0	1.161154	0	0
95.0	1.161154	1	1
96.0	1.161154	0	0
97.0	1.161154	0	0
98.0	1.161154	0	0
99.0	1.161154	0	0
100.0	1.161154	0	0
112.0	0	1	1
115.0	0	1	1
118.0	0	1	1
160.0	0	1	1
195.0	0	1	1
213.0	0	1	1
234.0	0	1	1
268.0	0	1	1
313.0	0	1	1