https://hydra-genetics-snv-indels.readthedocs.io

🐍 hydra-genetics/snv_indels

Snakemake module containing steps to call snv and small indels

💬 Introduction

The module contains rules to call variants from .bam-files per chromosome, merging the resulting .vcf-files, fixing the allele frequency field followed by decomposing and normalizing steps to finally combine the results from different callers using an ensemble approach. Available callers are Mutect2, Freebayes and VarDict and Haplotypecaller. Mutect2 is also used to generate a genomic .vcf-file.

❗ Dependencies

In order to use this module, the following dependencies are required:

Note! Releases of snv_indels <= v0.2.0 needs tabulate<0.9.0 added in requirements.txt*

🎒 Preparations

Sample and unit data

Input data should be added to samples.tsv and units.tsv. The following information need to be added to these files:

Column Id	Description
samples.tsv
sample	unique sample/patient id, one per row
tumor_content	ratio of tumor cells to total cells
units.tsv
sample	same sample/patient id as in samples.tsv
type	data type identifier (one letter), can be one of Tumor, Normal, RNA
platform	type of sequencing platform, e.g. NovaSeq
machine	specific machine id, e.g. NovaSeq instruments have @Axxxxx
flowcell	identifer of flowcell used
lane	flowcell lane number
barcode	sequence library barcode/index, connect forward and reverse indices by +, e.g. ATGC+ATGC
fastq1/2	absolute path to forward and reverse reads
adapter	adapter sequences to be trimmed, separated by comma

Reference data

A reference .fasta-file should be specified in config.yaml in the section reference and fasta. In addition, the file should be indexed using samtools faidx and the path of the resulting file added to the stanza fai. A bed file containing the covered regions shall be added to design_bed.

✅ Testing

The workflow repository contains a small test dataset .tests/integration which can be run like so:

$ cd .tests/integration
$ snakemake -s ../../Snakefile -j1 --use-singularity

🚀 Usage

To use this module in your workflow, follow the description in the snakemake docs. Add the module to your Snakefile like so:

module snv_indels:
    snakefile:
        github(
            "hydra-genetics/snv_indels",
            path="workflow/Snakefile",
            tag="v0.1.0",
        )
    config:
        config


use rule * from snv_indels as snv_indels_*

Compatibility

Latest:

• alignment:v0.5.1

See COMPATIBLITY.md file for a complete list of module compatibility.

Output files

The following output files should be targeted via another rule:

File	Description
snv_indels/bcbio_variation_recall_ensemble/{sample}_{type}.ensembled.vcf.gz	combined .vcf generated by ensemble
snv_indels/{caller}/{sample}_{type}.normalized.sorted.vcf.gz	sorted .vcf.gz for each caller
snv_indels/gatk_mutect2_gvcf/{sample}_{type}.merged.g.vcf.gz	genomic .vcf
snv_indels/deepvariant/{sample}_{type}.merged.vcf.gz	deepvariant .vcf.gz
snv_indels/deepvariant/{sample}_{type}.merged.g.vcf.gz	genomic .g.vcf.gz for deepvariant
snv_indels/glnexus/{sample}_{type}.vcf.gz	trio .vcf.gz with proband sample id generated by glnexus from deeptrio genomic .g.vcf.gz

🧑‍⚖️ Rule Graph