Hi all, I'm trying "raredisease" for the first time. But I'm getting some some errors at startup.

params.svdb_query_bedpedbs or params.svdb_query_dbs should be set.                                                                                                                                 
params.vep_filters or params.vep_filters_scout_fmt should be set.                                                                                                                                  
params.intervals_wgs not set.                                                                                                                                                                      
params.intervals_y not set.                                                                                                                                                                        
params.vcfanno_resources not set.                                                                                                                                                                  
params.vcfanno_toml not set.                                                                                                                                                                       
params.score_config_snv not set.                                                                                                                                                                   
params.variant_consequences_snv not set.                                                                                                                                                           
params.score_config_sv not set.                                                                                                                                                                    
params.variant_consequences_sv not set.                                                                                                                                                            
params.ploidy_model not set.

and i'ts not clear to me what is the nature of all those options. For example

score_config_snv

is "SNV rank model config file for genmod", but what is the nature of this file ?

Hi @yokofakun, The score configuration essentially determines how each annotation is scored. It allows you to configure the weight each annotation carries in ranking your variants. You should be able to find more information about these parameters in here.

@Ram I'm sorry, I don't know how I skipped the information, the answer was right in front of me on the manual page ! Thank you Ram !

No problem @yokofakun! 🙂

Hello, I'm also trying to run this pipeline for the first time. I want to use the GRCh38 versions. I read the parameters doc above, and I was able to download a few of the files. But unfortunately, I don't have enough bioinformatics knowledge to know which files I should be downloading for some of the other required parameters... Would anyone be able to help? (Feel free to DM!) Thanks a lot!

params.vcfanno_resources not set.
params.vcfanno_toml not set.
params.vep_cache not set.
params.gnomad_af not set.
params.score_config_snv not set.
params.variant_consequences_snv not set.
params.score_config_sv not set.
params.variant_consequences_sv not set.
params.ploidy_model not set.
params.gcnvcaller_model not set.
params.readcount_intervals not set.
params.mobile_element_references not set.
params.mobile_element_svdb_annotations not set.