pairsamtools

pairsamtools is a set of simple and fast command-line tools to process sequencing data from Hi-C experiments.

pairsamtools operate on sequence alignments and perform the following operations:

• detect and classify ligation sites (a.k.a. Hi-C pairs) produced in Hi-C experiments

• sort Hi-C pairs for downstream analyses

• detect, tag and remove PCR/optical duplicates

• generate extensive statistics of Hi-C datasets

• select Hi-C pairs given flexibly defined criteria

• restore and tag .sam files for selected subsets of Hi-C pairs

pairsamtools produce .pairs files compliant with the 4DN standards.

Contents:

• Quickstart
  • Installation
• Parsing alignments into pairs
  • Overview
  • Terminology
  • Unmapped/multimapped reads
  • Multiple ligations (walks)
  • Interpreting gaps between alignments
  • Rescuing single ligations
  • Pair flipping
  • Other reporting options
• .pairsam format
  • specification
  • pair types
• Command-line tools
  • pairsamtools
    • dedup
    • filterbycov
    • markasdup
    • merge
    • parse
    • phase
    • restrict
    • select
    • sort
    • split
    • stats

Indices and tables

• Index

• Module Index

• Search Page