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 _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
