Annovar_Whitelist_Filter_WDL
WDL that runs Annovar and a filtering R Script on the output of Mutect2
This WDL workflow can also be found on dockstore: https://dockstore.org/my-tools/registry.hub.docker.com/ccondon/whitelist_filter
The Annovar task uses an official perl image: https://hub.docker.com/_/perl
The WhitelistFilter task uses a custom docker image with R 4.1.0 and needed packages installed: https://hub.docker.com/repository/docker/ccondon/whitelist_filter
annovar_whitelist_filter.wdl
** ANNOVAR **
Annovar functionally annotates genetic variants detected from diverse genomes. Given a list of variants with chromosome, start position, end position, reference nucleotide and observed nucleotides, Annovar can perform gene-based annotation, region-based annotation, filter-based annotation, and more.
See ANNOVAR documentation to fully understand functionality: https://annovar.openbioinformatics.org/en/latest/user-guide/startup/
annovar_zip: the zipped folder with all of the needed files to run Annovar
- NOTE: This file path is set on Terra - The file must be in the Workspace's bucket
annovar_vcf_input: the Tables/sample column containing the vcf output files from a run of Mutect2
- NOTE: This is set on Terra (ex. this.filtered_vcf)
annovar_protocols: the specificed protocols needed to run annovar (default = refGene,cosmic70)
- NOTE: You must add the needed file paths to annovar_data_sources
annovar_operation: the specified operations needed to run annovar (default = g,f)
- NOTE: They must match up with annovar_protocols
ref_name: the reference name needed for annovar to run (default = hg38)
annovar_docker: the docker image to be used in the Annovar task
** WHITELIST_FILTER **
WhitelistFilter filters annovar's output based on only relevant data to our lab's whitelist.
You can find the R script code with comments on github: https://github.com/charliecondon/Annovar_Whitelist_Filter_WDL
sample_id: set to the corresponding sample id for a given run
- NOTE: This is set on Terra (ex. this.sample_id)
whitelist_filter_zip: the zipped folder with all of the needed files, including the .R Script file, needed to run WhitelistFilter
- NOTE: This file path is set on Terra - The file must be in the Workspace's bucket
txt_input: the txt input file that was an output of annovar
whitelist_filter_docker: the docker image to be used in the Annovar task
** WDL OUTPUTS **
Four CSV files:
- one with the whitelist filter applied
- one ready for manual review
- one with variant count information for debugging
- one with all the pre-whitelist variants listed