Python postcall_annotate Examples

Example #1

File: variation.py Project: mcicdata/bcbb

def finalize_genotyper(call_file, bam_file, ref_file, config):
    """Perform SNP genotyping and analysis.
    """
    vrn_files = configured_vrn_files(config, ref_file)
    variantcaller = config["algorithm"].get("variantcaller", "gatk")
    if variantcaller in ["freebayes", "cortex"]:
        call_file = freebayes.postcall_annotate(call_file, ref_file, vrn_files, config)
    filter_snp = variant_filtration(call_file, ref_file, vrn_files, config)
    phase_snp = phasing.read_backed_phasing(filter_snp, bam_file, ref_file, config)
    _eval_genotyper(phase_snp, ref_file, vrn_files.dbsnp, config)
    return phase_snp

Example #2

File: variation.py Project: rwness/bcbb

def finalize_genotyper(call_file, bam_file, ref_file, config):
    """Perform SNP genotyping and analysis.
    """
    vrn_files = configured_vrn_files(config, ref_file)
    variantcaller = config["algorithm"].get("variantcaller", "gatk")
    if variantcaller in ["freebayes", "cortex", "samtools"]:
        call_file = freebayes.postcall_annotate(call_file, ref_file, vrn_files, config)
    filter_snp = variant_filtration(call_file, ref_file, vrn_files, config)
    phase_snp = phasing.read_backed_phasing(filter_snp, bam_file, ref_file, config)
    _eval_genotyper(phase_snp, ref_file, vrn_files.dbsnp, config)
    return phase_snp