Somatic WGS SV Calling

Implementation of the somatic_wgs_sv_calling step

The somatic_wgs_sv_calling step takes as the input the results of the ngs_mapping step (aligned NGS reads) and performs somatic SV calling on them. The result are called SVs in VCF format.

Step Input

The variant annotation step uses Snakemake sub workflows for using the result of the ngs_mapping step.

Step Output

For each tumor DNA NGS library with name lib_name/key lib_pk and each read mapper mapper that the library has been aligned with, and the variant caller var_caller, the pipeline step will create a directory output/{mapper}.{var_caller}.{lib_name}-{lib_pk}/out with symlinks of the following names to the resulting VCF, TBI, and MD5 files.

{mapper}.{var_caller}.{lib_name}-{lib_pk}.vcf.gz
{mapper}.{var_caller}.{lib_name}-{lib_pk}.vcf.gz.tbi
{mapper}.{var_caller}.{lib_name}-{lib_pk}.vcf.gz.md5
{mapper}.{var_caller}.{lib_name}-{lib_pk}.vcf.gz.tbi.md5

For example, it might look as follows for the example from above:

output/
+-- bwa.manta.P001-T1-DNA1-WGS1-4
|   `-- out
|       |-- bwa.manta.P001-T1-DNA1-WGS1-4.vcf.gz
|       |-- bwa.manta.P001-T1-DNA1-WGS1-4.vcf.gz.tbi
|       |-- bwa.manta.P001-T1-DNA1-WGS1-4.vcf.gz.md5
|       `-- bwa.manta.P001-T1-DNA1-WGS1-4.vcf.gz.tbi.md5
[...]

Generally, these files will be unfiltered, i.e., contain low-quality variants and also variants flagged as being non-somatic.

Global Configuration

The static_data_config/reference/path has to be configured with the path to the reference FASTA file.

Default Configuration

The default configuration is as follows.

# Default configuration somatic_wgs_sv_calling
step_config:
  somatic_wgs_sv_calling:
    path_ngs_mapping: ../ngs_mapping  # REQUIRED
    tools: [manta]  # REQUIRED - available: 'delly2' and 'manta'
    delly2:
      path_exclude_tsv: null  # optional
      max_threads: 16

Somatic WGS SV Calling

Step Input

Step Output

Global Configuration

Default Configuration

Available Somatic CNV Callers

Reports