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, 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
