SMaHT Pipelines Documentation

Welcome to the documentation for SMaHT analysis pipelines and associated resources.

CONTENTS

PREPROCESSING

• FASTQ Files

  • polyG Artifacts Removal

ALIGNMENT

• Short-Read Illumina, Paired-End

  • Alignment
  • Read Groups
  • Duplicate Reads
  • Local Realignment
  • Base Quality Score Recalibration
  • Hi-C

• Long-Read PacBio HiFi

  • Alignment
  • Read Groups
  • Methylation and Tags

• Long-Read Oxford Nanopore

  • Alignment
  • Read Groups
  • Methylation and Tags

ANALYSIS

• Short-Read RNA-seq, Paired-End

  • Alignment
  • Duplicate Reads
  • Transcript Quantification
  • Gene Quantification

• Long-Read RNA-seq, PacBio Kinnex

  • Read Clustering
  • Alignment
  • Transcript Collapsing
  • Isoform Classification and Filtering
  • Read Annotation

• Germline Variant Calling, DNAscope Hybrid

  • Phased Germline Variants

• SMaHT Single-Nucleotide Variant Calling

  • Short-Read Variant Calling
  • Long-Read Variant Calling
  • Calls Merging and Normalization
  • Hierarchical Filtering
  • Cross-Technology Validation
  • Donor-Level Refinement
  • Confidence Designation

REFERENCE FILES

• Genome Builds

  • Build GRCh38

• Genome Annotations

  • GENCODE

• Variant Catalogs

  • Single Nucleotide Polymorphism Database
  • Mills and 1000 Genomes Project
  • gnomAD Population Allele Frequencies for Mutect2
  • Brain Somatic Mosaicism Network Panel of Normals

• Software Specific

  • Burrows-Wheeler Transform Index
  • STAR Index
  • RSEM Reference

Release CHANGELOG