All Published Workflows
19 workflows that have been reviewed and published
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
Variant Allele Frequency Lookup from gnomAD using RocksDB
Fast look up interface allel frequency of variants from gnomad with rocksdb.
conda install -c conda-forge python-rocksdb
pip ...
M. tuberculosis variant identification (deprecated 2023). Use: https://github.com/ksw9/mtb-vars
Snakemake pipeline for M. tuberculosis variant identification from short-read data, mapping with bwa, variant identificat...
Snakemake workflow for annotating and filtering variant data
Snakemake workflow for annotating and filtering variant data in small families according to different inheritance patterns...
Snakemake GATK best-practices workflow for variant calling
This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. In
Snakemake workflow: dna-seq-gatk-variant-calling
This Snakemake pipeline implements the GATK best-practices workflow for calling small germline variants. The usage of thi...
Variant Calling Workflow for Joint Multi-Sample VCF Generation
Forked from https://gitlab.com/data-analysis5/dna-sequencing/54gene-wgs-germline This workflow is designed to take either fas...
Variant-calling-pipeline for identifying strain specific variants
A reproducible snakemake workflow for identifying strain specific variants in Danio Rerio (Zebrafish). Variants called would ...
GATK Best-Practices Pipeline for Small Genomic Variant Calling
This Snakemake pipeline implements the GATK best-practices workflow for calling small genomic variants. It's based on t...
SpliceAI Variant Lookup and Prediction with RocksDB
Fast look up interface and prediction for missing variants in look table for spliceAI with rocksdb. Clone this git repository:
Re-running Genetic Variation Analysis
Code_for_Genetic_Diversity_SAmpling How to re-run the 'genetic variation' analysis described in Madupe et al 2023 The details...
Variant Filtering Module for VCF Files with Region and Annotation Filters
Collection of variant filters The module consists of rules used to filter VCF files. Currently the VCFs can be filtered based...