def run_rnaseq_ann_filter(data): """Run RNA-seq annotation and filtering. """ data = to_single_data(data) if dd.get_vrn_file(data): eff_file = effects.add_to_vcf(dd.get_vrn_file(data), data)[0] if eff_file: data = dd.set_vrn_file(data, eff_file) ann_file = population.run_vcfanno(dd.get_vrn_file(data), data) if ann_file: data = dd.set_vrn_file(data, ann_file) variantcaller = dd.get_variantcaller(data) if variantcaller and ("gatk-haplotype" in variantcaller): filter_file = variation.gatk_filter_rnaseq(dd.get_vrn_file(data), data) data = dd.set_vrn_file(data, filter_file) # remove variants close to splice junctions vrn_file = dd.get_vrn_file(data) vrn_file = variation.filter_junction_variants(vrn_file, data) data = dd.set_vrn_file(data, vrn_file) return [[data]]