resequencing

Overview ¶

Implementation (work in progress) of the resequencing analysis pipeline used to teach the introductory NGS bioinformatics analysis course at SciLifeLab as described on this page: https://scilifelab.github.io/courses/ngsintro/1502/labs/resequencing-analysis

Prerequisites: Samtools, BWA, Picard, GATK. You can install all tools except GATK on X/L/K/Ubuntu, with this command:

sudo apt-get install samtools bwa picard-tools

GATK needs to be downloaded and installed manually from: http://www.broadinstitute.org/gatk