We have a bunch of WGS samples and would like to import them in genomicsDBimport before joint genotyping. We are for this project interested in coding sequences. Is it better :
-Lwith gencode coding sequences annotation and put
To split the analysis and execute one instance of genomicsDBimport per chromosome (e.g.
-L chr1). My idea would be to use a job-array on my local slurm cluster (one job per chromosome). But what about the merging ? Should I put the same -
-genomicsdb-workspace-pathfor all jobs then ?
version of GATK : 4.1