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 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):
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
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