ntakebay
commented
4 years ago - Paralleliziation can be done at Haplotype_Caller (HC_PARALLELIZE) stage or Genomics_DB_Import/Genotype_GVCFs stage (PARALLELIZE). I generalized the method implemented for PBS, so it can be used for both with and without PBS. It required fair amount of structural change, but I also reduced the redundant codes to make it easier to maintain.
- If intervals file are specified in .bed format instead of .list/.intervals, it now converts to .list format internally to make processing easier.
- With WGS analysis, it used to ignore PARALLELIZE variable in Config, but now it can do non-parallelized analysis (not particularly useful, but the process represents Config better, so users might be less surprised).
- Genotype_GVCFs with WGS makes separate vcf files corresponding to each chromosome (with parallelization). The output used to be in Genotype_GVCFs directory, but now they are located in Genotype_GVCFs/vcf_split_regions subdirectory. This seems to be more consistent with the targeted analysis, and makes it easier to implement the following option a little bit.
- One additional option GG_COMBINED_VCF was added. It it is set to true, all separate vcf files in Genotype_GVCFs/vcf_split_regions get combined into a single vcf file, Genotype_GVCFs/raw_variants.vcf, at the end of Genotype_GVCFs handler.
- Finally a few bugs were fixed; .bed file can contain more than 3 columns now, path/file name can contain -, it should behave better when filenames contains white spaces, etc.