chiara111p111
commented
3 months ago COSE DA FARE: OncoKB Annotation for SNV, Fusions and Copy Number; Discretization of copy number variants based on cellularity (optional) or seg.mean; Fix gnomAD annotation for new release of VEP; Dockerization ; Fixed bugs in versioning; Fixed bugs in update, remove and delete functions; Made the various modules callable individually (ex. Make tables , Make meta files or Filter variants) ; Extreme customization of possible filters (adding new input arguments, see later) ; Changes in input arguments:
- removed "filter-vcf" argument (to filter non mutated positions in vcf). It is now the default but with some checks needed
- Introduction of --Filter arg, which accepts a string for specifying all desired filters (p -> filter==PASS,:white_check_mark: b- > Benign , v-> vaf, o-> Oncokb , g -> gnomAD, q > Consequence, y-> polyphen # s -> clin_sig) ( We could use the FPG workflow as default)
- Intro of "--Metafile" to use functions for metafiles;
- Intro of "--FilterOnly" to use functions for filtering SNVs;
- Intro of "--multiple" , if input VCF contains multiple samples (SNV only);
- Changes of "--type" argument. Now accepts also "tab" and "fus" to execute only "make tables" part and "fusion" part, respectively;
- Create a unique folder to store filtered MAF files;
- Change of input file format for TMB/MSI/Fusion ( From CombinedOutput like format to Folder/Table);
- Ongoing: Adding validate folder from cbioportal script ⛅ /
- Minor customisation in VCF2MAF script
- In conf.ini : adding new parameters for filters, max of vaf , oncoKB key etc
- Creating templates for multi-samples VCF, MSI, TMB, Fusion
- If patient ID is missing, Sample ID is used for both columns (as suggested by the reviewer)
lucianogiaco
LorenzoBioinfo
.