SNP calling from NGS data

Prerequisites

  • Data sets from the previous session “Mapping NGS Data.”  We can provide this on a flash drive at the beginning of the course if you missed the previous session or were unable to complete the exercises.

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. SNP_calling
  2. run_snpcalling.sh
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