def run_rnaseq_ann_filter(data): """Run RNA-seq annotation and filtering. """ ann_file = vcfanno.run_vcfanno(dd.get_vrn_file(data), ["rnaedit"], data) if ann_file: dd.set_vrn_file(data, ann_file) filter_file = variation.gatk_filter_rnaseq(dd.get_vrn_file(data), data) dd.set_vrn_file(data, filter_file) return [[data]]
def run_rnaseq_ann_filter(data): """Run RNA-seq annotation and filtering. """ data = to_single_data(data) if dd.get_vrn_file(data): 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) return [[data]]
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]]
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]]
def variant_filtration(call_file, ref_file, vrn_files, data, items): """Filter variant calls using Variant Quality Score Recalibration. Newer GATK with Haplotype calling has combined SNP/indel filtering. """ caller = data["config"]["algorithm"].get("variantcaller") if "gvcf" not in dd.get_tools_on(data): call_file = ploidy.filter_vcf_by_sex(call_file, items) if caller in ["freebayes"]: return vfilter.freebayes(call_file, ref_file, vrn_files, data) elif caller in ["platypus"]: return vfilter.platypus(call_file, data) elif caller in ["samtools"]: return vfilter.samtools(call_file, data) elif caller in ["gatk", "gatk-haplotype", "haplotyper"]: if dd.get_analysis(data).lower().find("rna-seq") >= 0: from bcbio.rnaseq import variation as rnaseq_variation return rnaseq_variation.gatk_filter_rnaseq(call_file, data) else: return gatkfilter.run(call_file, ref_file, vrn_files, data) # no additional filtration for callers that filter as part of call process else: return call_file