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Snakemake pipelines for Variant calling

Usage

1. Edit the config.yaml file for required files:

Install snakemake, ensembl-vep first.

update the path to:

  • BAM_DIR
  • GENOME
  • VEP

And the output directory:

  • BCFTOOL (bcftools pipeline)

    • WORKSPACE

  • GATK (gatk pipeline)

    • WORKSPACE

2 Run on local computer

# modify the file path in haplomap and run with 12 cores
snakemake -s bcftools.call.smk  --configfile config.yaml \
          -k -p -j 12

or

# modify the file path in haplomap and run with 12 cores
snakemake -s gatk.call.smk  --configfile config.yaml \
          -k -p -j 12

About variant calling pipeline:

  1. bcftools call
  • prefered pipeline for inbred mouse and haplomap input
  1. GATK best practice
  • designed for human genetics
  • users are responsible for tuning VQSR or hardfiltering parameters if use non-human data

Caution !: Both pipelines take a long time to run.

Ensemble VEP

Install VEP

Download and Install

or use conda to install vep

Install Genome

Install data for offline mode

INSTALL.pl -a cfp -s mus_musculus -y GRCm38 --CONVERT --PLUGINS CADD,GO,TSSDistance,LoF,SpliceAI

or Human

INSTALL.pl -a cfp -s homo_sapiens -y GRCh38 --CONVERT

Annotation

e.g

bcftools view -f .,PASS ${input.vcf} | \
        ${params.VEPBIN}/vep --fasta ${input.reference} ${params.genome_build} \
        --format vcf --fork ${threads} --hgvs --force_overwrite \
        --uniprot --domains --symbol --regulatory --distance 1000 --biotype \
        --gene_phenotype MGI --check_existing  --pubmed --numbers \
        --offline --cache --variant_class \
        --gencode_basic --no_intergenic --individual all \
        -o ${output} --tab --compress_output gzip \

Notes

Why not GATK for inbred population ?

One of my colleague who studies mouse genetics, said,

I tried the haplotype caller from GATK. But it seems that the haplotype caller is designed for heterogeneous genome like human than for mice. Therefore, the result coming out of HC is worse than samtools, as I manually inspected a few regions that HC calls didn't make sense.

In addition, in one of their mouse genomic paper that we reviewed, they even skipped the second recalibration step. We asked them why and they said it was because of the same reason: good for human but not that good for the homogeneous inbred mouse.

However, my experiences with GATK (>v4.0) is as good as bcftools.