Changes between Initial Version and Version 1 of StructuralVariationPipeline


Ignore:
Timestamp:
Nov 3, 2011 11:30:13 AM (13 years ago)
Author:
Leon Mei
Comment:

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  • StructuralVariationPipeline

    v1 v1  
     1This page summaries the SV pipelines used in GoNL
     2
     3== SV modules ==
     4Because of different coverage, the following software are used to call SVs from GoNL data.
     5* Pindel: Eric-Wubbo, Kai
     6* DWAQseq/1-2-3 SV: Victor, Slavik
     7* Breakdancer: Jayne, Joep
     8* GenomeSTRiP: Bob, Laurent
     9* CNVnater: Abdel
     10
     11The following software are used to assemble reads to detect novel (large) insertions.
     12* soapdenovo: Victor
     13* Abyss: Aby
     14
     15== Pilot phase ==
     1616 trios, 4 quartets are used for pilot test. Here are the software setup.
     17
     18==== Pindel ====
     19
     20==== DWAQseq/1-2-3 SV ====
     21
     22==== Breakdancer ====
     23
     24==== GenomeSTRiP ====
     25
     26==== CNVnater ====
     27
     28==== soapdenovo ====
     29
     30==== Abyss ====
     31
     32
     33== Production phase ==
     34UMCG BAMs to be used for production calls.
     35
     36==== Pindel ====
     37
     38==== DWAQseq/1-2-3 SV ====
     39
     40==== Breakdancer ====
     41
     42==== GenomeSTRiP ====
     43
     44==== CNVnater ====
     45
     46==== soapdenovo ====
     47
     48==== Abyss ====