Repositories list

• PipelineNGSpublic

  Public
  Pipeline for variant calling in NGS data based on GATK's best practices.

  0•0•0•0•Updated Jun 21, 2024Jun 21, 2024

• MosaiQC-public

  Public template
  SmartCleaning (now called MosaiQC) is a script developed by Thiago Peixoto Leal to clean and perform QC of genotyping array data using PLINK. It automates the different steps. If interested in using SmartCleaning, contact the LDGH/Mosaico Translational Genomics team ([email protected] )

  0•0•0•0•Updated Jan 23, 2024Jan 23, 2024

• .github

  Public
  0•0•0•0•Updated Mar 13, 2023Mar 13, 2023

• NAToRA_Public

  Public
  NAToRA toolkit consists of a series of scripts to execute kinship control analyses as described in the manuscript by Leal et al. 2022, entitled "NAToRA, a relatedness-pruning method to minimize the loss of dataset size in genetic and omics analyses"

  Python

  •1•4•0•0•Updated Jan 12, 2023Jan 12, 2023

• 3A-public

  Public
  0•0•0•0•Updated Oct 11, 2022Oct 11, 2022

• Genotype-Imputation-public

  Public
  Public description of LDGH Genotype Imputation v.2. pipeline developed in Phyton by Thiago Peixoto Leal, with the collaboration by Nathalia M. Araujo, Marilia Scliar and Ricardo Lyra. The user may choose to use SHAPEIT2 or SHAPEIT4 for haplotype inferences, and IMPUTE2 or IMPUTE4 for imputation. For further details or if you are interested in us…

  bioinformaticsgwaspopulation-genetics+ 1genotype-imputation

  0•2•0•0•Updated Aug 31, 2022Aug 31, 2022

• CNVice

  Public
  R

  •0•0•0•0•Updated Aug 23, 2022Aug 23, 2022

• NAToRASimulator

  Public
  Python

  •0•0•0•0•Updated Mar 30, 2022Mar 30, 2022

• Population-Structure

  Public
  Population Structure scripts

  0•0•0•0•Updated Sep 6, 2018Sep 6, 2018

• Genotype_Correction

  Public
  Python

  •0•0•0•0•Updated May 30, 2018May 30, 2018

• Targeted_Sequencing_Pipeline

  Public
  Perl

  •0•0•0•0•Updated May 18, 2018May 18, 2018