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Aligned.out_merged.metrics.txt
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## htsjdk.samtools.metrics.StringHeader
# MarkDuplicates INPUT=[Aligned.out_merged.sorted.bam] OUTPUT=Aligned.out_merged.dedup.bam METRICS_FILE=Aligned.out_merged.metrics.txt 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 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_INDEX=false 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 Apr 28 14:41:10 EET 2019
## 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 0 35702 3610 0 0 6121 0 0.171447 91843
## HISTOGRAM java.lang.Double
BIN VALUE all_sets non_optical_sets
1.0 0.999998 24442 24442
2.0 1.677916 4372 4372
3.0 2.137488 634 634
4.0 2.449041 94 94
5.0 2.660248 26 26
6.0 2.803429 4 4
7.0 2.900494 3 3
8.0 2.966296 3 3
9.0 3.010905 1 1
10.0 3.041146 0 0
11.0 3.061647 0 0
12.0 3.075545 0 0
13.0 3.084966 0 0
14.0 3.091353 1 1
15.0 3.095683 0 0
16.0 3.098619 1 1
17.0 3.100609 0 0
18.0 3.101958 0 0
19.0 3.102872 0 0
20.0 3.103492 0 0
21.0 3.103912 0 0
22.0 3.104197 0 0
23.0 3.10439 0 0
24.0 3.104521 0 0
25.0 3.10461 0 0
26.0 3.10467 0 0
27.0 3.104711 0 0
28.0 3.104739 0 0
29.0 3.104758 0 0
30.0 3.10477 0 0
31.0 3.104779 0 0
32.0 3.104785 0 0
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100.0 3.104797 0 0