caballero/snakemake-varcall

Simple snakemake workflow for WGS variant calling

Simple Snakemake pipeline to do Variant Calling

Process

Preparations

1. Genome needs to be indexed for BWA, fasta and index is defined in config file
2. Fastq files are located in a directory defined in config, it expects a SAMPLEID1_1.fastq.gz and SAMPLEID1_2.fastq.gz file names
3. All processes and results are stored by -d parameter in SnakeMake
4. All logs are stored under log/ directory
5. Dependencies can be added in a conda environment as defined in envs/environment_varcall.yaml for running in local mode, or as modules load to be used with --use-envmodules
6. The pipeline can be run in a cluster (--slurm) if configured properly
7. Almost all jobs are requesting 10 cores, but can be scaled with --cores N parameter

Input configuration

Defined in config.yaml, it requires

samples:
  - sampleID1
  - sampleID2
fastq_dir: /path/to/fastq/dir
genome: /path/to/genome.fa
bcf_mpileup_param: "params for bcftools mpileup"
bcf_call_param: "params for bcftools call"
bcf_norm_param: "params for bcftools norm"
bcf_filter_param: "params for bcftools filters"

Execution

snakemake <params> -d results --configfile config.yaml

Trio phasing of variants

Process

Preparations

1. Input files are BCF files from the previous workflow
2. All processes and results are stored by -d parameter in SnakeMake
3. All logs are stored under log/ directory
4. Dependencies can be added in a conda environment as defined in envs/environment_trio_filtering.yaml for running in local mode, or as modules load to be used with --use-envmodules
5. The pipeline can be run in a cluster (--slurm) if configured properly
6. Almost all jobs are requesting 1 core, but can be scaled with --cores N parameter

Input configuration

Defined in config.yaml, it requires

mother_id: MOM_ID
mother_bcf: /path/to/mother.bcf
father_id: DAD_ID
father_bcf: /path/to/father.bcf
child_id: KID_ID
child_bcf: /path/to/child.bcf

Execution

snakemake -s workflow/trio_filtering.smk <params> -d results --configfile config_trio.yaml

(C) Juan Caballero 2024