(snps, indels) génétiques analyse de variants
Post on 21-Oct-2021
4 Views
Preview:
TRANSCRIPT
Analyse de variants génétiques
(SNPs, indels)
Gautier Sarah - Alexis Dereeper – Christine Tranchant Formation Bio-informatique - Thiès 2018
Global BAM with read group
Cutadapt
Mapping BWA
VCF file
Fastq (RC1)
BAM with read group
Mapping BWA
Fastq (RC2)
BAM with read group
Mapping BWA
Fastq (RC3)
BAM with read group
Mapping BWA
Fastq (RC4)
BAM with read group
mergeSam
Add or Replace GroupsAdd or Replace Groups Add or Replace Groups Add or Replace Groups
Cutadapt Cutadapt Cutadapt
Haplotypes and phasing
•
•
Gautier Sarah - Alexis Dereeper – Christine Tranchant Formation Bio-informatique - Thiès 2018
SNP annotation using SnpEff
•…
•
Gautier Sarah - Alexis Dereeper – Christine Tranchant Formation Bio-informatique - Thiès 2018
Projet Gigwa, pour la gestion des données massives de variants (GBS, RADSeq, WGRS)
Gautier Sarah - Alexis Dereeper – Christine Tranchant Formation Bio-informatique - Thiès 2018
Gautier Sarah - Alexis Dereeper – Christine Tranchant Formation Bio-informatique - Thiès 2018
Gautier Sarah - Alexis Dereeper – Christine Tranchant Formation Bio-informatique - Thiès 2018
Comparison between individuals
Diversity analysis
Gautier Sarah - Alexis Dereeper – Christine Tranchant Formation Bio-informatique - Thiès 2018
Gautier Sarah - Alexis Dereeper – Christine Tranchant Formation Bio-informatique - Thiès 2018
Gautier Sarah - Alexis Dereeper – Christine Tranchant Formation Bio-informatique - Thiès 2018
Différenciation génétique de la souris domestique (Bonhomme et al, 2010)
Gautier Sarah - Alexis Dereeper – Christine Tranchant Formation Bio-informatique - Thiès 2018
GWAS (Genome-Wide Association Studies)
Gautier Sarah - Alexis Dereeper – Christine Tranchant Formation Bio-informatique - Thiès 2018
GWAS issues
…
•ooo
Gautier Sarah - Alexis Dereeper – Christine Tranchant Formation Bio-informatique - Thiès 2018
Study of root characters using GWAS in Oryza sativa japonica. Influence of a correction using structure and kinship
Gautier Sarah - Alexis Dereeper – Christine Tranchant Formation Bio-informatique - Thiès 2018
Exemple du Riz: 3000 genomes+ HDRA (High density Rice Array)
Gautier Sarah - Alexis Dereeper – Christine Tranchant Formation Bio-informatique - Thiès 2018
Exemple du Riz: 3000 genomes+ HDRA (High density Rice Array)
Gautier Sarah - Alexis Dereeper – Christine Tranchant Formation Bio-informatique - Thiès 2018
Exemple du Riz: 3000 genomes+ HDRA (High density Rice Array)
Gautier Sarah - Alexis Dereeper – Christine Tranchant Formation Bio-informatique - Thiès 2018
SNiPlay: Web application for polymorphism analyses
Alexis Dereeper – Christine Tranchant Formation Bio-informatique IRD Ouagadougou 2016
Gautier Sarah - Alexis Dereeper – Christine Tranchant Formation Bio-informatique - Thiès 2018
Gautier Sarah - Alexis Dereeper – Christine Tranchant Formation Bio-informatique - Thiès 2018
top related