def run_rnaseq_variant_calling(data): """ run RNA-seq variant calling, variation file is stored in `vrn_file` in the datadict """ variantcaller = dd.get_variantcaller(data) if isinstance(variantcaller, list) and len(variantcaller) > 1: logger.error("Only one variantcaller can be run for RNA-seq at " "this time. Post an issue here " "(https://github.com/bcbio/bcbio-nextgen/issues) " "if this is something you need to do.") sys.exit(1) if variantcaller: if "gatk-haplotype" in variantcaller: data = variation.rnaseq_gatk_variant_calling(data) if vardict.get_vardict_command(data): data = variation.rnaseq_vardict_variant_calling(data) if dd.get_vrn_file(data): ann_file = vcfanno.run_vcfanno(dd.get_vrn_file(data), ["rnaedit"], data) if ann_file: data = dd.set_vrn_file(data, ann_file) ann_file = population.run_vcfanno(dd.get_vrn_file(data), data, population.do_db_build([data])) if ann_file: data = dd.set_vrn_file(data, ann_file) return [[data]]
def run_rnaseq_variant_calling(data): variantcaller = dd.get_variantcaller(data) if isinstance(variantcaller, list) and len(variantcaller) > 1: logger.error("Only one variantcaller can be run for RNA-seq at " "this time. Post an issue here " "(https://github.com/chapmanb/bcbio-nextgen/issues) " "if this is something you need to do.") sys.exit(1) if variantcaller and "gatk" in variantcaller: data = variation.rnaseq_gatk_variant_calling(data) if vardict.get_vardict_command(data): data = variation.rnaseq_vardict_variant_calling(data) return [[data]]
def run_rnaseq_variant_calling(data): """ run RNA-seq variant calling, variation file is stored in `vrn_file` in the datadict """ variantcaller = dd.get_variantcaller(data) if isinstance(variantcaller, list) and len(variantcaller) > 1: logger.error("Only one variantcaller can be run for RNA-seq at " "this time. Post an issue here " "(https://github.com/bcbio/bcbio-nextgen/issues) " "if this is something you need to do.") sys.exit(1) if variantcaller: if "gatk-haplotype" in variantcaller: data = variation.rnaseq_gatk_variant_calling(data) if vardict.get_vardict_command(data): data = variation.rnaseq_vardict_variant_calling(data) vrn_file = dd.get_vrn_file(data) return [[data]]
def run_rnaseq_variant_calling(data): """ run RNA-seq variant calling, variation file is stored in `vrn_file` in the datadict """ variantcaller = dd.get_variantcaller(data) if isinstance(variantcaller, list) and len(variantcaller) > 1: logger.error("Only one variantcaller can be run for RNA-seq at " "this time. Post an issue here " "(https://github.com/chapmanb/bcbio-nextgen/issues) " "if this is something you need to do.") sys.exit(1) if variantcaller and "gatk" in variantcaller: data = variation.rnaseq_gatk_variant_calling(data) if vardict.get_vardict_command(data): data = variation.rnaseq_vardict_variant_calling(data) # annotate RNA-editing events with vcfanno if dd.get_vrn_file(data): vrn_file = vcfanno.run_vcfanno(dd.get_vrn_file(data), "rnaedit", data) data = dd.set_vrn_file(data, vrn_file) return [[data]]
def run_rnaseq_variant_calling(data): variantcaller = dd.get_variantcaller(data) if variantcaller and "gatk" in variantcaller: data = variation.rnaseq_gatk_variant_calling(data) return [[data]]