This page summaries the SV pipelines used in GoNL

SV tasks

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

• Pindel: Eric-Wubbo, Kai
• DWAC-seq/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

PCR/chip validation is performed by Wigard, Johan.

Pilot phase (Sep, Oct 2011)

16 trios, 4 quartets are used for pilot test. Refer to the sample file for detailed sample IDs.

Pindel

• used command line

• result location

DWAC-seq/1-2-3 SV

Breakdancer

GenomeSTRiP

CNVnater

soapdenovo

Abyss

Validation (Oct 2011)

TBA

Production phase (Nov, Dec 2011)

UMCG BAMs to be used for production calls.

Pindel

• used command line

DWAC-seq/1-2-3 SV

Breakdancer

GenomeSTRiP

CNVnater

soapdenovo

Abyss