def run_varscan(align_bams, items, ref_file, assoc_files, region=None, out_file=None): if is_paired_analysis(align_bams, items): call_file = samtools.shared_variantcall(_varscan_paired, "varscan", align_bams, ref_file, items, assoc_files, region, out_file) else: call_file = samtools.shared_variantcall(_varscan_work, "varscan", align_bams, ref_file, items, assoc_files, region, out_file) return call_file
def run_varscan(align_bams, items, ref_file, assoc_files, region=None, out_file=None): paired = get_paired_bams(align_bams, items) if paired and paired.normal_bam and paired.tumor_bam: call_file = samtools.shared_variantcall(_varscan_paired, "varscan", align_bams, ref_file, items, assoc_files, region, out_file) else: vcfutils.check_paired_problems(items) call_file = samtools.shared_variantcall(_varscan_work, "varscan", align_bams, ref_file, items, assoc_files, region, out_file) return call_file
def run_varscan(align_bams, items, ref_file, assoc_files, region=None, out_file=None): if len(align_bams) == 2 and all(item["metadata"].get("phenotype") is not None for item in items): call_file = samtools.shared_variantcall(_varscan_paired, "varscan", align_bams, ref_file, items, assoc_files, region, out_file) else: call_file = samtools.shared_variantcall(_varscan_work, "varscan", align_bams, ref_file, items, assoc_files, region, out_file) return call_file
def run_varscan(align_bams, items, ref_file, assoc_files, region=None, out_file=None): if len(align_bams) == 2 and all( item["metadata"].get("phenotype") is not None for item in items): call_file = samtools.shared_variantcall(_varscan_paired, "varscan", align_bams, ref_file, items, assoc_files, region, out_file) else: call_file = samtools.shared_variantcall(_varscan_work, "varscan", align_bams, ref_file, items, assoc_files, region, out_file) return call_file
def run_varscan(align_bams, ref_file, config, dbsnp=None, region=None, out_file=None): call_file = samtools.shared_variantcall(_varscan_work, "varscan", align_bams, ref_file, config, dbsnp, region, out_file) return call_file
def run_varscan(align_bams, items, ref_file, assoc_files, region=None, out_file=None): call_file = samtools.shared_variantcall(_varscan_work, "varscan", align_bams, ref_file, items[0]["config"], assoc_files, region, out_file) return call_file
def run_varscan(align_bams, ref_file, config, dbsnp=None, region=None, out_file=None): call_file = samtools.shared_variantcall( _varscan_work, "varscan", align_bams, ref_file, config, dbsnp, region, out_file ) _fix_varscan_vcf(call_file, align_bams) return call_file