Blog

• One year of Nextflow

  Automating large analyses (workflows) is the epitome of bioinformatics. I started using the workflow manager and language Nextflow a little bit more than one year ago, so I would like to make a report of my usage and opinion with it.

  I had previously used Snakemake, but felt some limitations [...]

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• Pre-filtering variants from VCFs: switching to bcftools

  I am currently (re)familiarizing with VCF files and their processing.

  It happens that they are many softwares to process them, in particular bcftools, vcftools (which are quite different from the former but whose functionalities overlap), and also GATK.

  My current work is to update an existing workflow from the [...]

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• False-Discovery rate correction for Hardy-Weinberg tests on a VCF

  It is common to apply a “quality check” filter on a VCF file to retain only variants that do not depart from a neutrality expectation, namely the Hardy-Weinberg equilibrium (HWE). In fact it’s also a way to discard potential genotyping errors. Note that the Hardy-Weinberg test can be two-sided [...]

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• TP de biostatistiques L3 - Cytomegalovirus humain

  Le cytomégalovirus humain, (HCMV) ou Human Herpesvirus 5 est un virus de la famille des herpès virus très fréquent dans la population humaine, mais qui passe généralement inaperçu. Il est transmis par contact via sécrétions corporelles. Ce TP est basé sur le jeu de donnée généré par Stockdale et al. 2018, légèrement modifié pour des besoins pédagogiques. Objectif: pour comprendre par quels facteurs le HCMV peut être responsable d’une mortalité accrue, on veut caractériser l’interaction du HCMV avec d’autres infections transmissibles comme le VIH et la tuberculose, ainsi qu’avec des facteurs de risques cardiovasculaires.

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• Softwares for computing different types of summary trees from MCMC samples

  How to build consensus trees from a Bayesian sample of phylogenetic trees. Main statistical concepts and which programs to use: Majority Rule, Maximum a posteriori, Maximum Clade Credibility.

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