## htsjdk.samtools.metrics.StringHeader # MarkDuplicates INPUT=[S41F.sorted.bam] OUTPUT=../output/11-RNAseq-snps/S41F.dedup.bam METRICS_FILE=../output/11-RNAseq-snps/S41F.dup_metrics.txt REMOVE_DUPLICATES=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 ADD_PG_TAG_TO_READS=true ASSUME_SORTED=false DUPLICATE_SCORING_STRATEGY=SUM_OF_BASE_QUALITIES PROGRAM_RECORD_ID=MarkDuplicates PROGRAM_GROUP_NAME=MarkDuplicates READ_NAME_REGEX= OPTICAL_DUPLICATE_PIXEL_DISTANCE=100 MAX_OPTICAL_DUPLICATE_SET_SIZE=300000 VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=STRICT COMPRESSION_LEVEL=2 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: Wed Mar 09 12:13:31 PST 2022 ## 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 1945233 16370998 11451332 9570203 862769 4457726 65273 0.281897 24542958 ## HISTOGRAM java.lang.Double BIN CoverageMult all_sets optical_sets non_optical_sets 1.0 1.002816 10502940 0 10543862 2.0 1.517489 1014966 60589 981808 3.0 1.781634 177099 1387 171360 4.0 1.917201 63175 268 62188 5.0 1.986778 33674 97 33305 6.0 2.022486 21251 40 21127 7.0 2.040813 14716 20 14579 8.0 2.050219 10815 10 10810 9.0 2.055046 8467 15 8369 10.0 2.057524 6573 4 6543 11.0 2.058795 5342 2 5307 12.0 2.059448 4427 2 4428 13.0 2.059783 3792 2 3764 14.0 2.059955 3320 1 3303 15.0 2.060043 2852 2 2846 16.0 2.060088 2516 1 2508 17.0 2.060111 2103 1 2094 18.0 2.060123 1951 2 1924 19.0 2.060129 1813 0 1810 20.0 2.060132 1647 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