Variant calling index

List of exercises

About

A generic variant calling workflow consists of the following basic steps:

1. read quality control and filtering
2. read mapping
3. removal / marking of duplicate reads
4. joint / sample-based variant calling and genotyping

There are different tweaks and additions to each of these steps, depending on application and method. The variant calling exercises here present the basic steps to go from raw data to variant calls.

The exercises are based on the Monkeyflowers dataset. Make sure to read the dataset document before running any commands as it will give you the biological background and general information about where to find and how to setup the data. We will focus on the red and yellow ecotypes in what follows.

Intended learning outcomes

• Perform qc on sequencing reads and interpret results
• Prepare reference for read mapping
• Map reads to reference
• Mark duplicates
• Perform raw variant calling to generate a set of sites to exclude from recalibration
• Perform base quality score recalibration
• Perform variant calling on base recalibrated data
• Do genotyping on all samples and combine results to a raw variant call set

Listing

Additional material

Variant calling, long description

Describes all steps of a standard variant calling workflow from data preparation to final summary QC. All commands are run manually without the aid of a workflow manager. From earlier course round.