Version 52 (modified by Morris Swertz, 14 years ago) (diff)


SNP calling pipeline

Status: Alpha Authors: Freerk van Dijk, Morris Swertz

This is the documentation of the BBMRI-NL snp calling pipeline based on the Broad GATK. It consists of the following three workflows:

Schematic Overview

This simplified overview this schema hides intermediate sort and indexing steps and only shows data inputs/outputs first time they occur.

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  • How long takes alignment per genome?
    • If this takes very long we can split read files
  • How long takes realign knownsonly (per genome)?
    • If very long, we need to rewrite workflow 2 to split before realign
  • For realign: if we split per chromosome, can we also split bam file?
  • How to easily lift over from b36 to b37
    • Contact BGI if they can use b37??


  • Recode workflow 2 to work per genome instead of per chromosome

List of steps

Attachments (3)

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