Welcome to Dovetail Page for Genetic Variation documentation

Overview

• Dovetail™ LinkPrep® assay is designed for the rapid generation of genomic interaction data specifically designed for the detection of genetic variants

• Key benefits of LinkPrep:

  • Compressed overall workflow to single day compared to 2-5 day workflow of other Hi-C approaches

  • Flexible input requirements

  • Improved mapping rate and even genomic coverage result in more complete contact matrices enabling variant detection similar to shotgun libraries

• This guide will take you step by step on how to process and QC your LinkPrep library, how to interpret the QC results, how to generate contact maps, and how to perform genetic variant detection. If you don’t yet have a sequencing LinkPrep library and you want to get familiar with the data, you can download LinkPrep sequence libraries from our publicly available data sets.

• The QC process starts with aligning the reads to a reference genome then retaining high quality mapped reads. From there the mapped data will be used to generate a pairs file with pairtools, which categorizes pairs by read type and insert distance, this step both flags and removes PCR duplicates. Once pairs are categorized, counts of each class are summed and reported.

• If this is your first time following this tutorial, please check the Before you begin page first.

Contents:

• Before you begin
  • Have a copy of the VariLink scripts on your machine:
  • Dependencies
  • Input files
  • Pre-alignment
• From fastq to final valid pairs bam file
  • fastq to final valid pairs bam file - step by step
• Alignment and Proximity-Ligation QC
  • Complexity
  • QC Assessment
  • Sequencing Recommendations
• Generating Contact Matrix
  • Generating HiC contact maps using Juicer tools
  • Generating cooler contact maps
• Detection of Genetic Variants
  • Example input files (.mcool, .hic, or bam files)
  • Calling Structural Variants
  • Calling Copy Number Variation
  • Calling SNVs and Indels
• VariLink Data Sets
• Support

Indices and tables

• Index

• Module Index

• Search Page