Filter variant calls using Variant Quality Score Recalibration.

    Newer GATK with Haplotype calling has combined SNP/indel filtering.

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