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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.
