README.md

Population joint SNP calling snakemake pipeline

This pipeline is inspired by F.J. Yang (Bioinplant Lab, Zhejiang University).

Dependent Software

• fastp
• BWA
• GATK
• samtools
• VCFtools
• bgzip

What the pipeline does

• Genome file index creation (BWA/samtools/GATK)
• Resequencing reads quality control
• Resequencing reads map to reference genome
• GATK SNP and INDEL calling pipeline
• SNP quality control (Missing rate, MAF etc.)

What to input

• Reference genome file
• WGS fastq files

What to output

• Basic set of SNP and INDEL (filtered with missingrate < 0.9 and MAF > 0.0005)
• Core set of SNP (filtered with missingrate < 0.9 and MAF > 0.05, could be used for population structure analysis)

Usage

1. Prepare your working directory

├── raw_data
├── genome_index
└── logs

Please storage your resequence data in raw_data/ folder and genome file in genome_index/ folder. Script files, pipeline files and configuration files can be stored the way you like.

2. Prepare the config file

The config file needs to be at the same folder of snakefile.

2.1 Move the genome file to genome_index/ folder and add the genome fasta file absolute path like:

# Absolute path to the genome fasta file
ref: "/workingdir/genome_index/genome.fasta" 

And chromosome IDs to genotype variants by per chromosomes to parallise the process.

chromosomes:
    - Chr01_hap1
    - Chr02_hap1
    - Chr03_hap1
    - ...
    - Chrnn_hap1

You can use the following command to generate the list.

cat /workingdir/genome_index/genome.fasta | grep ">" | awk '{gsub(/^>/, "    - "); print}'

2.2 Sometimes the fastq files may be ended with .fastq.gz or .fq.gz, specify the suffix of the fastq files if it's necessary.

# Fastq file suffix
fastq_suffix: " " # Default value is ".fq.gz"

2.3 Fill in the name of the samples. The samples name need to be filled with specific format like:

# Sample list, samples' name should start with letters.
sample:
    - sample1
    - sample2
    - sample3
    - sample4
    - ...
    - samplen

You can use following command to add sample list to the config file if you have a sample list txt file (for example sample.list):

# sample.list
sample1
sample2
sample3
sample4

# Add samples to the config file:
sed 's/^/    - /' sample.list >> ${working_dir}/SNPcalling_config.yaml

3. Submit the pipeline to HPC cluster

For example:

snakemake \
	--snakefile ${working_dir}/00-script/snake_pipeline/${snakemake_file} \
	-d ${working_dir} \
	--cores ${cores_num} \
	--rerun-incomplete \
	--latency-wait 360 \
	--keep-going