def _post_filter_freebayes(orig_file, ref_file, broad_runner): """Perform basic sanity filtering of FreeBayes results, removing low confidence calls. """ in_file = apply("{0}-raw{1}".format, os.path.splitext(orig_file)) _move_vcf(orig_file, in_file) filters = ["QUAL < 20.0", "DP < 5"] filter_file = genotype.variant_filtration_with_exp(broad_runner, in_file, ref_file, "", filters) _move_vcf(filter_file, orig_file)
def postcall_filter(in_file, ref_file, vrn_files, config): """Perform quality score filtering on FreeBayes variant calls. """ out_file = _check_file_gatk_merge(in_file) out_file = annotation.annotate_dbsnp(out_file, vrn_files.dbsnp, ref_file, config) filters = ["QUAL < 20.0", "DP < 5"] out_file = genotype.variant_filtration_with_exp(broad.runner_from_config(config), out_file, ref_file, "", filters) return out_file
def postcall_filter(in_file, ref_file, vrn_files, config): """Perform quality score filtering on FreeBayes variant calls. """ out_file = _check_file_gatk_merge(in_file) out_file = annotation.annotate_dbsnp(out_file, vrn_files.dbsnp, ref_file, config) filters = ["QUAL < 20.0", "DP < 5"] out_file = genotype.variant_filtration_with_exp( broad.runner_from_config(config), out_file, ref_file, "", filters) return out_file