samleenz/variant-calling

variant calling + processing pipline based in Snakemake

variant-calling

author: Sam Lee

code provided as-is where-is etc

Simple variant calling pipeline for RNA-seq data. Implemented using Opossum and Platypus for data preparation and variant calling.

A VCF of all variants and a gzipped VCF per chromosme will be produced.

Usage

# install Snakemake if needed 
#  (easiest through conda)
#  (all other dependencies managed by conda)
conda create -n myEnv Snakemake
source activate myEnv

Snakemake --use-conda --cores N

In config.yaml bamDir should point to the directory with the aligned + sorted bam files for the analysis.

samples is then a dictionary with key:value pairs of sample:sample-bam-file although the value doesn't really matter as the Snakefile expects the input to be of the format {sample}_Aligned.sortedByCoord.out.bam

To do

• Write rule for mapping of fastq files with STAR
• Decide on imputation method and implement