SNP calling from NGS data

Prerequisites

  • The four bam files from the previous session “Mapping NGS Data.” Please let us know before class if you missed the previous session or were unable to complete the exercises so we can make sure you have the necessary files.

Topics covered

  • Overview of SNP calling tools for NGS data
  • SNP calling using GATK and Samtools
  • SNP annotation and effect prediction with SnpEff

Estimated Time

  • Lecture and examples: 2:00 h

Materials

  1. slides
  2. run_snpcalling.sh
  3. run_snpeff.sh
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