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LIBD73-170118_HC73J_LIBD73_L003.0006.bam --INPUT LIBD73-170118_HC73J_LIBD73_L003.0004.bam --INPUT LIBD73-170118_HC73J_LIBD73_L003.0005.bam --INPUT LIBD73-170118_HC73J_LIBD73_L003.0003.bam --INPUT LIBD73-170118_HC73J_LIBD73_L003.0009.bam --INPUT LIBD73-170118_HC73J_LIBD73_L003.0007.bam --INPUT LIBD73-170118_HC73J_LIBD73_L003.0008.bam --INPUT LIBD73-170118_HC73J_LIBD73_L003.0010.bam --INPUT LIBD73-170118_HC73J_LIBD73_L003.0012.bam --INPUT LIBD73-170118_HC73J_LIBD73_L003.0011.bam --INPUT LIBD73-170118_HC73J_LIBD73_L004.0005.bam --INPUT LIBD73-170118_HC73J_LIBD73_L004.0006.bam --INPUT LIBD73-170118_HC73J_LIBD73_L004.0004.bam --INPUT LIBD73-170118_HC73J_LIBD73_L004.0002.bam --INPUT LIBD73-170118_HC73J_LIBD73_L004.0001.bam --INPUT LIBD73-170118_HC73J_LIBD73_L004.0003.bam --INPUT LIBD73-170118_HC73J_LIBD73_L004.0010.bam --INPUT LIBD73-170118_HC73J_LIBD73_L004.0008.bam --INPUT LIBD73-170118_HC73J_LIBD73_L004.0007.bam --INPUT LIBD73-170118_HC73J_LIBD73_L004.0011.bam --INPUT LIBD73-170118_HC73J_LIBD73_L004.0012.bam --INPUT LIBD73-170118_HC73J_LIBD73_L004.0009.bam --INPUT LIBD73-170118_HC73J_LIBD73_L005.0001.bam --INPUT LIBD73-170118_HC73J_LIBD73_L005.0005.bam --INPUT LIBD73-170118_HC73J_LIBD73_L005.0002.bam --INPUT LIBD73-170118_HC73J_LIBD73_L005.0009.bam --INPUT LIBD73-170118_HC73J_LIBD73_L005.0003.bam --INPUT LIBD73-170118_HC73J_LIBD73_L005.0008.bam --INPUT LIBD73-170118_HC73J_LIBD73_L005.0007.bam --INPUT LIBD73-170118_HC73J_LIBD73_L005.0006.bam --INPUT LIBD73-170118_HC73J_LIBD73_L005.0010.bam --INPUT LIBD73-170118_HC73J_LIBD73_L005.0012.bam --INPUT LIBD73-170118_HC73J_LIBD73_L005.0011.bam --INPUT LIBD73-170118_HC73J_LIBD73_L006.0004.bam --INPUT LIBD73-170118_HC73J_LIBD73_L006.0002.bam --INPUT LIBD73-170118_HC73J_LIBD73_L005.0004.bam --INPUT LIBD73-170118_HC73J_LIBD73_L006.0003.bam --INPUT LIBD73-170118_HC73J_LIBD73_L006.0001.bam --INPUT LIBD73-170118_HC73J_LIBD73_L006.0005.bam --INPUT LIBD73-170118_HC73J_LIBD73_L006.0007.bam --INPUT LIBD73-170118_HC73J_LIBD73_L006.0009.bam --INPUT LIBD73-170118_HC73J_LIBD73_L006.0006.bam --INPUT LIBD73-170118_HC73J_LIBD73_L006.0011.bam --INPUT LIBD73-170118_HC73J_LIBD73_L006.0008.bam --INPUT LIBD73-170118_HC73J_LIBD73_L006.0010.bam --INPUT LIBD73-170118_HC73J_LIBD73_L006.0012.bam --INPUT LIBD73-170118_HC73J_LIBD73_L007.0003.bam --INPUT LIBD73-170118_HC73J_LIBD73_L007.0004.bam --INPUT LIBD73-170118_HC73J_LIBD73_L007.0002.bam --INPUT LIBD73-170118_HC73J_LIBD73_L007.0001.bam --INPUT LIBD73-170118_HC73J_LIBD73_L007.0005.bam --INPUT LIBD73-170118_HC73J_LIBD73_L007.0007.bam --INPUT LIBD73-170118_HC73J_LIBD73_L007.0009.bam --INPUT LIBD73-170118_HC73J_LIBD73_L007.0008.bam --INPUT LIBD73-170118_HC73J_LIBD73_L007.0012.bam --INPUT LIBD73-170118_HC73J_LIBD73_L008.0002.bam --INPUT LIBD73-170118_HC73J_LIBD73_L007.0006.bam --INPUT LIBD73-170118_HC73J_LIBD73_L007.0011.bam --INPUT LIBD73-170118_HC73J_LIBD73_L007.0010.bam --INPUT LIBD73-170118_HC73J_LIBD73_L008.0001.bam --INPUT LIBD73-170118_HC73J_LIBD73_L008.0007.bam --INPUT LIBD73-170118_HC73J_LIBD73_L008.0006.bam --INPUT LIBD73-170118_HC73J_LIBD73_L008.0005.bam --INPUT LIBD73-170118_HC73J_LIBD73_L008.0004.bam --INPUT LIBD73-170118_HC73J_LIBD73_L008.0008.bam --INPUT LIBD73-170118_HC73J_LIBD73_L008.0010.bam --INPUT LIBD73-170118_HC73J_LIBD73_L008.0011.bam --INPUT LIBD73-170118_HC73J_LIBD73_L008.0012.bam --INPUT LIBD73-170118_HC73J_LIBD73_L008.0009.bam --INPUT LIBD73-170118_HC73J_LIBD73_L008.0003.bam --OUTPUT LIBD73.md.bam --METRICS_FILE LIBD73.md.cram.metrics --REMOVE_DUPLICATES false --TMP_DIR . --VALIDATION_STRINGENCY LENIENT --REFERENCE_SEQUENCE chm13v2.0.XY.fasta --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 --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 --COMPRESSION_LEVEL 2 --MAX_RECORDS_IN_RAM 500000 --CREATE_INDEX false --CREATE_MD5_FILE false --help false --version false --showHidden false --USE_JDK_DEFLATER false --USE_JDK_INFLATER false PN:MarkDuplicates @PG ID:samtools.1 PN:samtools PP:samtools VN:1.17 CL:samtools view -Ch -T chm13v2.0.XY.fasta -o LIBD73.md.cram LIBD73.md.bam @PG ID:samtools.2 PN:samtools PP:samtools.2P VN:1.17 CL:samtools view -Ch -T chm13v2.0.XY.fasta -o LIBD73.md.cram LIBD73.md.bam @PG ID:samtools.3 PN:samtools PP:samtools.2Q VN:1.17 CL:samtools view -Ch -T chm13v2.0.XY.fasta -o LIBD73.md.cram LIBD73.md.bam @PG ID:samtools.4 PN:samtools PP:samtools.2R VN:1.17 CL:samtools view -Ch -T chm13v2.0.XY.fasta -o LIBD73.md.cram LIBD73.md.bam @PG ID:samtools.5 PN:samtools PP:samtools.2S VN:1.17 CL:samtools view -Ch -T chm13v2.0.XY.fasta -o LIBD73.md.cram LIBD73.md.bam @PG ID:samtools.6 PN:samtools PP:samtools.2T VN:1.17 CL:samtools view -Ch -T chm13v2.0.XY.fasta -o LIBD73.md.cram LIBD73.md.bam @PG ID:samtools.7 PN:samtools PP:samtools.2U VN:1.17 CL:samtools view -Ch -T chm13v2.0.XY.fasta -o LIBD73.md.cram LIBD73.md.bam @PG ID:samtools.8 PN:samtools PP:samtools.2V VN:1.17 CL:samtools view -Ch -T chm13v2.0.XY.fasta -o LIBD73.md.cram LIBD73.md.bam @PG ID:samtools.9 PN:samtools PP:samtools.2W VN:1.17 CL:samtools view -Ch -T chm13v2.0.XY.fasta -o LIBD73.md.cram LIBD73.md.bam @PG ID:samtools.10 PN:samtools PP:samtools.2X VN:1.17 CL:samtools view -Ch -T chm13v2.0.XY.fasta -o LIBD73.md.cram LIBD73.md.bam @PG ID:samtools.11 PN:samtools PP:samtools.2Y 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