SNV_indels module

The snv_indels module consists of a number of variant callers for:

• Short-read (SR) data, both somatic and germline variants,

• Long-read (LR) data, both somatic and germline variants. Most of the variant callers for LR data are based on deep-learning models.

Some tools are able to handle data from tumor-only (TO) samples, while others require matched normal (MN) samples.

Somatic calls can be made by: - freebayes, mutect2, vardict, deepsomatic, clairs-to.

Germline calls can be produced by: - haplotypecaller, deepvariant, deeptrio, glnexus.
The module also provide tools for:

• variant decomposition and normalization with VT (applicable to both SR and LR data),

• aggregation of the results from different callers into an ensemble with bc_bio (only for SR data),

• sorting and indexing of the variants with bcftools (applicable to both SR and LR data),

• predict which somatic variants are likely to be mosaicisms with deepmosaic or mosaicforecast (applicable to both SR and LR data),

• read-based phasing of variants and haplotagging of reads with whatshap (applicable to both SR and LR data).
  

The module is designed to be used in a snakemake pipeline and can be easily integrated into existing pipelines that follow the logic of hydra-genetics.

Hydra-genetics

We are an organization/community with the goal of making snakemake pipeline development easier, faster, a bit more structured and of higher quality.

We do this by providing snakemake modules that can be combined to create a complete analysis or included in already existing pipelines. All modules are subjected to extensive testing to make sure that new releases doesn't unexpectedly break existing pipeline or deviate from guidelines and best practices on how to write code.