Germline Variant Annotation
Implementation of the variant_annotation
step
The variant_annotation
step takes as the input the results of the variant_calling
step
(called germline variants in vcf.gz format) and annotates the variants, e.g., using VEP.
Stability
TBD
Step Input
The variant annotation step uses Snakemake sub workflows for using the result of the
variant_calling
step.
Step Output
TBD
Global Configuration
TBD
Default Configuration
The default configuration is as follows.
# Default configuration variant_annotation
step_config:
variant_annotation:
path_variant_calling: ../variant_calling
tools:
- vep
vep:
# We will always run VEP in cache mode. You have to provide the directory to the
# cache to use (VEP would be ``~/.vep``).
cache_dir: null # OPTIONAL
# The cache version to use. gnomAD v2 used 85, gnomAD v3.1 uses 101.
cache_version: "85"
# The assembly to use. gnomAD v2 used "GRCh37", gnomAD v3.1 uses "GRCh38".
assembly: "GRCh37"
# The flag selecting the transcripts. One of "gencode_basic", "refseq", and "merged".
tx_flag: "gencode_basic"
# Number of threads to use with forking, set to 0 to disable forking.
num_threads: 16
# Additional flags.
more_flags: "--af_gnomade --af_gnomadg"
# The --buffer_size parameter
buffer_size: 100000
Available Variant Annotators
The following variant annotator is currently available:
"vep"
: See the software documentation for more details
Reports
N/A