Wrapper for Variant-Caller execution
Run the desired variant caller and takes as argument the BAM / CRAM, the reference genome and other options depending on the variant caller
-vc VARIANT_CALLER, --variant_caller VARIANT_CALLER | help: the path to the variantcaller installation folder
--vc_path VC_PATH | help: the required option when you do not find the path of variantcaller
-g GENOME_REF, --genome_ref GENOME_REF | help: the reference genome file
-b BAM, --bam BAM | help: the bam file
-v VCF, --vcf VCF | help: the output vcf file
-s SAMPLE, --sample SAMPLE | help: Sample name to use in the output VCF file
--slurm | help: Required option when you want to run multiple jobs
-N NODE, --node NODE | help: the number of nodes used
-c CORE, --core CORE | help: the number of cores used
-t THREAD, --thread THREAD | help: the number of threads used
-be BED, --bed BED | help: the bed file containing target regions
-l {DEBUG,INFO,WARNING,ERROR}, --logging-level {DEBUG,INFO,WARNING,ERROR} | help: The logger level. [Default: DEBUG]
Development in progress -