hydra-genetics

alignment

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

long_read

cnv_sv

Collection of rules used to call structural variants

annotation

Collections of rules to annotate vcf files.

parabricks

Snakemake module containing different analyses provided by parabricks.

docker

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

snv_indels

Collection of rules used to call snv and small indels.

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.

misc

qc

Collection of rules performing QC and generating reports.

fusions

fusions

gitaction-testing

filtering

compression

Snakemake module containing steps to minimize big files prior to storage

mitochondrial

Snakemake module for performing Mitochondrial short variant discovery

sentieon

biomarker

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

reports

Snakemake module for generating reports related to Hydra-Genetics results

references

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

prealignment

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

.github

Organization information

multipass

vagrant

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

profiles

Example of configuration profiles for executing Snakemake in various computing environments