wiki:SnpCallingPipeline

Version 54 (modified by Morris Swertz, 12 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.

Error: Failed to load processor graphviz
No macro or processor named 'graphviz' found

Discussion

  • 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??

Todo:

  • Recode workflow 2 to work per genome instead of per chromosome
  • QC pipeline
    • Simple SNP caller
    • GATK variant eval to make venn diagrams
    • Contact Yurii for this; Let Jeroen take charge?

List of steps

Attachments (3)

Download all attachments as: .zip