Python gatk_joint_calling Examples

Example #1

File: rnaseq.py Project: dh10/bcbio-nextgen

def run_rnaseq_joint_genotyping(*samples):
    data = samples[0][0]
    variantcaller = dd.get_variantcaller(data)
    ref_file = dd.get_ref_file(data)
    out_file = os.path.join(dd.get_work_dir(data, "."), "variation", "combined.vcf")
    if variantcaller and "gatk" in variantcaller:
        vrn_files = [dd.get_vrn_file(d) for d in dd.sample_data_iterator(samples)]
        out_file = variation.gatk_joint_calling(data, vrn_files, ref_file, out_file)
        updated_samples = []
        for data in dd.sample_data_iterator(samples):
            data = dd.set_square_vcf(data, out_file)
            updated_samples.append([data])
        return updated_samples
    return samples

Example #2

File: rnaseq.py Project: nickholz/bcbio-nextgen

def run_rnaseq_joint_genotyping(*samples):
    data = samples[0][0]
    variantcaller = dd.get_variantcaller(data)
    ref_file = dd.get_ref_file(data)
    out_file = os.path.join(dd.get_work_dir(data, "."), "variation", "combined.vcf")
    if variantcaller and "gatk" in variantcaller:
        vrn_files = [dd.get_vrn_file(d) for d in dd.sample_data_iterator(samples)]
        out_file = variation.gatk_joint_calling(data, vrn_files, ref_file, out_file)
        updated_samples = []
        for data in dd.sample_data_iterator(samples):
            data = dd.set_square_vcf(data, out_file)
            updated_samples.append([data])
        return updated_samples
    return samples

Example #3

File: rnaseq.py Project: DoaneAS/bcbio-nextgen

def run_rnaseq_joint_genotyping(*samples):
    data = samples[0][0]
    variantcaller = dd.get_variantcaller(data)
    if not variantcaller:
       return samples
    if "gatk" not in variantcaller:
        return samples
    ref_file = dd.get_ref_file(data)
    if variantcaller and "gatk" in variantcaller:
        vrn_files = [dd.get_vrn_file(d) for d in dd.sample_data_iterator(samples)]
        out_file = variation.gatk_joint_calling(data, vrn_files, ref_file)
        vrn_file = vcfanno.run_vcfanno(out_file, ["rnaedit"], data)
        updated_samples = []
        for data in dd.sample_data_iterator(samples):
            data = dd.set_square_vcf(data, vrn_file)
            updated_samples.append([data])
        return updated_samples
    return samples

Example #4

def run_rnaseq_joint_genotyping(*samples):
    data = samples[0][0]
    variantcaller = dd.get_variantcaller(data)
    if not variantcaller:
       return samples
    if "gatk" not in variantcaller:
        return samples
    ref_file = dd.get_ref_file(data)
    if variantcaller and "gatk" in variantcaller:
        vrn_files = [dd.get_vrn_file(d) for d in dd.sample_data_iterator(samples)]
        out_file = variation.gatk_joint_calling(data, vrn_files, ref_file)
        vrn_file = vcfanno.run_vcfanno(out_file, "rnaedit", data)
        updated_samples = []
        for data in dd.sample_data_iterator(samples):
            data = dd.set_square_vcf(data, vrn_file)
            updated_samples.append([data])
        return updated_samples
    return samples