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.
step_config:
somatic_wgs_sv_calling:
#path_ngs_mapping: ../ngs_mapping
#tools: # Options: 'manta', 'delly2'
# - manta
#manta: {}
#delly2:
# path_exclude_tsv:
# max_threads: 16
Available Somatic CNV Callers
The following somatic SV callers are currently available
"manta"
"delly2"
Reports
Currently, no reports are generated.