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)
# no additional filtration for callers that filter as part of call process
elif caller in ["samtools", "varscan", "mutect"]:
return call_file
else:
config = data["config"]
snp_file, indel_file = vcfutils.split_snps_indels(
call_file, ref_file, config)
snp_filter_file = _variant_filtration_snp(snp_file, ref_file,
vrn_files, data)
indel_filter_file = _variant_filtration_indel(indel_file, ref_file,
vrn_files, data)
orig_files = [snp_filter_file, indel_filter_file]
out_file = "{base}combined.vcf".format(
base=os.path.commonprefix(orig_files))
return vcfutils.combine_variant_files(orig_files, out_file, ref_file,
config)
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 ["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 ["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, config):
"""Filter variant calls using Variant Quality Score Recalibration.
Newer GATK with Haplotype calling has combined SNP/indel filtering.
"""
caller = config["algorithm"].get("variantcaller")
if caller in ["freebayes"]:
return vfilter.freebayes(call_file, ref_file, vrn_files, config)
# no additional filtration for callers that filter as part of call process
elif caller in ["samtools", "varscan"]:
return call_file
else:
snp_file, indel_file = vcfutils.split_snps_indels(call_file, ref_file, config)
snp_filter_file = _variant_filtration_snp(snp_file, ref_file, vrn_files, config)
indel_filter_file = _variant_filtration_indel(indel_file, ref_file, vrn_files, config)
orig_files = [snp_filter_file, indel_filter_file]
out_file = "{base}combined.vcf".format(base=os.path.commonprefix(orig_files))
return vcfutils.combine_variant_files(orig_files, out_file, ref_file, config)
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
