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
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
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
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