Somatic WGS CNV Calling

Implementation of the somatic_wgs_cnv_calling step

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

Step Input

The variant annotation step uses Snakemake sub workflows for using the result of the ngs_mapping and somatic_variant_calling steps. Somatic (small) variant calling is required for b-allele based filtration. For the somatic variant calling, one somatic (small) variant caller must be configured of which to use the results.

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.canvas.P001-T1-DNA1-WGS1-4
|   `-- out
|       |-- bwa.canvas.P001-T1-DNA1-WGS1-4.vcf.gz
|       |-- bwa.canvas.P001-T1-DNA1-WGS1-4.vcf.gz.tbi
|       |-- bwa.canvas.P001-T1-DNA1-WGS1-4.vcf.gz.md5
|       `-- bwa.canvas.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

None so far

Default Configuration

The default configuration is as follows.

Available Somatic CNV Callers

The following somatic CNV callers are currently available

• "canvas"

Reports

Currently, no reports are generated.