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10x Genomics
Genome & Exome

Long Ranger , printed on 05/05/2025

PHASER_SVCALLER_CSPHASER_SVCALLERLOUPE_PREPROCESSPHASER_SVCALLER_PREFLIGHTPHASER_SVCALLER_PREFLIGHT_LOCALSUMMARIZE_REPORTS_COMBINED_SV_CALLERANALYZE_SV_COMBINED_CALLSMERGE_SV_CALLS3_STRUCTVAR_CALLERANALYZE_SV_CALLSCALL_STRUCTVARSCOUNT_READS_BCSDETECT_OVERLAPSFILTER_PILEUPSGET_DEL_CANDIDATES2GET_READPAIR_EVIDENCEGET_READPAIR_LOCIMERGE_SV_CALLSPREPARE_SVCALLING_RANGES_TERMINAL_CNV_CALLERANALYZE_TERMINAL_CNV_CALLSCALL_HMM_BC_CNVCOMPUTE_COVERAGE_SPIKESGET_COV_BEDGRAPH_WITH_ZOOMPREPARE_TERMINAL_CNV_GT_AND_BINSIZE_LINKED_READS_ALIGNERBARCODE_AWARE_ALIGNERMARK_DUPLICATESMERGE_BC_BAMMERGE_POS_BAM_FASTQ_PREP_NEWBUCKET_FASTQSSETUP_CHUNKSSORT_FASTQS_REPORTERCOPY_FRAGMENT_INFOFILTER_BARCODESREPORT_BASICREPORT_COVERAGEREPORT_LENGTH_MASS_SHORT_STRUCTVAR_CALLERANALYZE_SV_CALLS2ASSEMBLE_PHASED_DELETIONSGET_DEL_CANDIDATESGET_JOINT_READ_LRGET_READPAIR_LOCI2GET_SMALL_CANDIDATESMERGE_SIMPLEMERGE_SV_CALLS2PREPARE_SVCALLING_RANGES2_SNPINDEL_PHASERANALYZE_SNPINDEL_CALLSATTACH_PHASINGCALL_HAPLOID_SNPINDELSPHASE_SNPINDELSPOPULATE_INFO_FIELDSSORT_GROUND_TRUTH_SNPINDEL_CALLERCALL_SNPINDELSPOPULATE_INFO_FIELDS
←  PHASER_SVCALLER_CS

This is the main Long Ranger pipeline that performs alignment, variant calling, phasing, and structural variant calling on whole genome data. This outer wrapper pipeline prepares files for final output.