Tag: Targeted

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.

SampleSeq and SampleSeq2 – Optimal Subject Selection in Targeted and Whole Genome Sequencing Experiments

SampleSeq and SampleSeq2

:: DESCRIPTION

SampleSeq is a probability-based algorithm for selecting samples for a targeted resequencing experiment.

SampleSeq2 requires a squared matrix of pairwise distance among all subjects that are candidates for selection. The matrix can be generated by PLINK using GWAS data or by Idcoefs using pedigree information. These are explained in detail in Sections II and III.In Section IV, we describe how to use SampleSeq2 for subject selection. In Section V, we describe how to estimate the number of independent genomes in a subset of subjects.

::DEVELOPER

Chun Li, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 SampleSeq

:: MORE INFORMATION

Citation

Edwards TL, Li C (2012)
Optimized selection of unrelated subjects for whole genome sequencing studies of rare high-penetrance alleles.
Genet Epidemiol. 2012 Jul;36(5):472-9. doi: 10.1002/gepi.21641. Epub 2012 May 23.

 

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