natmurad / variantcalling

Workflow to perform a Variant Calling Analysis

🧬 Pedigree Analysis - Generate SNP Panel

Docker Environment

• Download the Dockerfile and inside same directory run:

docker build -t <IMAGE_TAG> .

• Check the IMAGE ID (look for the name of your image tag):

docker images -a

• Start container

docker run --name <CONTAINER_NAME> -it <IMAGE_ID> bash

• Copy your files to container

docker cp <DIRECTORY/FILES> <CONTAINER_ID>:<DIRECTORY>

variantCalling Workflow

Steps:

Input: sam files.

1 - Converts sam files to bam files

2 - Creates indexed bam files (bai) with samtools

3 - Performs variant calling with freebayes using a reference genome. It results in vcf files

4 - These files are compressed using bgzip and indexed using tabix

5 - Filter variants considering MAF, Hardy-Weinberg Equilibrium & missing variants proportion with Plink. This step generates a bed file

6 - Converts bed file back to vcf format also using Plink

7 - Compress and index filtered vcf files as in step 4

8 - Get the common variants considering all individuals of same family with bedtools isec

9 - Load the files with common SNPs of each family on R and analyse it (Venn graph and comparisons between families)

Prepare code before running:

Change in the file "variantCalling" the path to the config.yaml file.

In config.yaml file change the paths for all folder.

Run pipeline:

snakemake -s variantCalling -c 50