hydra-genetics

alignment

Snakemake module containing processing steps that should be performed during sequence alignment.

hydra-genetics

Command line interface to create new modules/pipelines or adding a new rule to a existing project. Helper libraries for handling samples and units.

mitochondrial

Snakemake module for performing Mitochondrial short variant discovery

annotation

Collections of rules to annotate vcf files.

cnv_sv

Collection of rules used to call structural variants

docker

Collection of dockerfiles with bioinformatic tools used to execute snakemake with singularity.

qc

Collection of rules performing QC and generating reports.

references

Collection of rules used to create references, panel of normals (PoN), and background filters.

biomarker

Collection of rules used to calculate biomarkers like MSI, TMB and HRD.

reports

Snakemake module for generating reports related to Hydra-Genetics results

filtering

.github

Organization information

compression

Snakemake module containing steps to minimize big files prior to storage

fusions

fusions

gitaction-testing

long_read

misc

multipass

parabricks

Snakemake module containing different analyses provided by parabricks.

prealignment

Snakemake module containing processing steps that should be performed before sequence alignment.

profiles

Example of configuration profiles for executing Snakemake in various computing environments

sentieon

snv_indels

Collection of rules used to call snv and small indels.

vagrant

Vagrant machine used to run snakemake/hydragenetics in combination with singularity on Windows/OSX