def variant_filtration(call_file, ref_file, vrn_files, data): """Filter variant calls using Variant Quality Score Recalibration. Newer GATK with Haplotype calling has combined SNP/indel filtering. """ caller = data["config"]["algorithm"].get("variantcaller") call_file = ploidy.filter_vcf_by_sex(call_file, data) 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 ["gatk", "gatk-haplotype"]: 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
def variant_filtration(call_file, ref_file, vrn_files, data): """Filter variant calls using Variant Quality Score Recalibration. Newer GATK with Haplotype calling has combined SNP/indel filtering. """ caller = data["config"]["algorithm"].get("variantcaller") call_file = ploidy.filter_vcf_by_sex(call_file, data) 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"]: 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
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