All Published Workflows
40 workflows that have been reviewed and published
A Snakemake pipeline for variant calling of genomic FASTQ data using GATK
This project is a snakemake workflow for processing .fastq.gz files and downstream analyses. The variant calling is prima...
Causal effect of modifiable risk factors on COVID
Esimating the shared genetic eitology and the causal association of potentially modifiable risk factors on SARS-CoV-2 infecti...
Analysis pipeline associated with master's thesis on the population structure, demographic history and distribution of fitness effects of birches in Scandinavia.
Code and supplementary associated with master's thesis on the population structure, demographic history and the distribution ...
Snakemake workflow: Meta-analysis of GWAS of gestational duration, preterm and post-term deliveries (EGG Consortium)
This repository contains code for Genetic effects on the timing of parturition and links to fetal birth weight .
Pol ...
Sample annotation
Analysis
Gene report
plink2
BCFtools
BEDTools
ggtree
GWAS
Pandas
pLink
Quant
Snakemake
Variant Effect Predictor (VEP)
coloc
cowplot
data.table
dendextend
dplyr
ggplot2
ggrepel
ggtern
gridExtra
kableExtra
knitr
metafor
plyr
scales
showtext
tidyr
tidyverse
numpy
scipy
Genetic variation
preeclampsia
Genomic prediction of amino acid traits in Arabidopsis seeds
Data and scripts necessary to run genomic partitioning and prediciton models on free amino acid traits measured in a diverse ...
Challenges of accurately estimating sex-biased admixture from X chromosomal and autosomal ancestry proportions
Models for estimating sex ratios assuming single pulse or constant admixture
Software requirements
Input...
Perform error-prone data preparation for whole genome regression modeling
An awesome whole genome regression modeling pipeline
This is the home of the pipeline, istari. Its long-term goals: ...
Multi-Step Genomic Analysis Pipeline for DeCOI WGS Cohort
Pipeline for QC, GWAS and gene-based collapsing within the DeCOI WGS cohort (1220 individuals). Rules for ROH-analysis and ge...
Snakemake Workflow: Impute HLA and/or KIR alleles from SNPs
N.B: As of 21st of February, 2020 shapeit=v2.r837 has been removed from the bioconda channel. Hence, I have removed it fr...