wiki:StructuralVariationPipeline

Version 1 (modified by Leon Mei, 11 years ago) (diff)

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This page summaries the SV pipelines used in GoNL

SV modules

Because of different coverage, the following software are used to call SVs from GoNL data.

  • Pindel: Eric-Wubbo, Kai
  • DWAQseq/1-2-3 SV: Victor, Slavik
  • Breakdancer: Jayne, Joep
  • GenomeSTRiP: Bob, Laurent
  • CNVnater: Abdel

The following software are used to assemble reads to detect novel (large) insertions.

  • soapdenovo: Victor
  • Abyss: Aby

Pilot phase

16 trios, 4 quartets are used for pilot test. Here are the software setup.

Pindel

DWAQseq/1-2-3 SV

Breakdancer

GenomeSTRiP

CNVnater

soapdenovo

Abyss

Production phase

UMCG BAMs to be used for production calls.

Pindel

DWAQseq/1-2-3 SV

Breakdancer

GenomeSTRiP

CNVnater

soapdenovo

Abyss