Sarek 2.7.1 – Detect Germline or Somatic Variants from Whole Genome or Targeted Sequencing

Sarek 2.7.1

:: DESCRIPTION

Sarek is a workflow designed to detect variants on whole genome or targeted sequencing data. Initially designed for Human, and Mouse, it can work on any species with a reference genome. Sarek can also handle tumour / normal pairs and could include additional relapses.

::DEVELOPER

the Science for Life Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Docker

:: DOWNLOAD

Sarek

:: MORE INFORMATION

Citation

Garcia M, Juhos S, Larsson M, Olason PI, Martin M, Eisfeldt J, DiLorenzo S, Sandgren J, Díaz De Ståhl T, Ewels P, Wirta V, Nistér M, Käller M, Nystedt B.
Sarek: A portable workflow for whole-genome sequencing analysis of germline and somatic variants.
F1000Res. 2020 Jan 29;9:63. doi: 10.12688/f1000research.16665.2. PMID: 32269765; PMCID: PMC7111497.

SegCNV – Detect Germline Copy Number Variations in SNP Array data

SegCNV

:: DESCRIPTION

SegCNV is a software package, implemented in C++, to detect germline copy number variations in SNP array data. Currently, SegCNV supports Illumina 550K and 610K genotyping platforms

::DEVELOPER

DCEG

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ compiler

:: DOWNLOAD

SegCNV

:: MORE INFORMATION

Citation

Genet Epidemiol. 2012 May;36(4):373-83. doi: 10.1002/gepi.21631.
An integrative segmentation method for detecting germline copy number variations in SNP arrays.
Shi J, Li P.

IgC2N – Identification of Germline Changes in Copy Number

IgC2N

:: DESCRIPTION

IgC2N is a three step computational framework to discover and genotype germline CNVs

::DEVELOPER

Demichelis Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux /Windows / MacOSX
R

:: DOWNLOAD

IgC2N

:: MORE INFORMATION

Citation:

PLoS One. 2011 Mar 29;6(3):e17539. doi: 10.1371/journal.pone.0017539.
A computational framework discovers new copy number variants with functional importance.
Banerjee S1, Oldridge D, Poptsova M, Hussain WM, Chakravarty D, Demichelis F.

GERMLINE 1.5.1 – Discovery Long Shared Segments of Identity by Descent (IBD) in large populations

GERMLINE 1.5.1

:: DESCRIPTION

GERMLINE is a program for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing.

::DEVELOPER

Sasha Gusev

:: SCREENSHOTS

N/A

::REQUIREMENTS

Linux

:: DOWNLOAD

GERMLINE

:: MORE INFORMATION

Citation

Gusev A, Lowe JK, Stoffel M, Daly MJ, Altshuler D, Breslow JL, Friedman JM, Pe’er I (2008)
Whole population, genomewide mapping of hidden relatedness.
Genome Research.2009 Feb;19(2):318-26.