def prepare_exclude_file(items, base_file, chrom=None):
"""Prepare a BED file for exclusion.
Excludes high depth and centromere regions which contribute to long run times and
false positive structural variant calls.
"""
items = shared.add_highdepth_genome_exclusion(items)
out_file = "%s-exclude%s.bed" % (utils.splitext_plus(base_file)[0],
"-%s" % chrom if chrom else "")
if not utils.file_exists(out_file) and not utils.file_exists(out_file +
".gz"):
with shared.bedtools_tmpdir(items[0]):
with file_transaction(items[0], out_file) as tx_out_file:
# Get a bedtool for the full region if no variant regions
want_bedtool = callable.get_ref_bedtool(
tz.get_in(["reference", "fasta", "base"], items[0]),
items[0]["config"], chrom)
want_bedtool = pybedtools.BedTool(
shared.subset_variant_regions(want_bedtool.saveas().fn,
chrom, tx_out_file, items))
sv_exclude_bed = _get_sv_exclude_file(items)
if sv_exclude_bed and len(want_bedtool) > 0:
want_bedtool = want_bedtool.subtract(
sv_exclude_bed, nonamecheck=True).saveas()
full_bedtool = callable.get_ref_bedtool(
tz.get_in(["reference", "fasta", "base"], items[0]),
items[0]["config"])
if len(want_bedtool) > 0:
full_bedtool.subtract(want_bedtool,
nonamecheck=True).saveas(tx_out_file)
else:
full_bedtool.saveas(tx_out_file)
return out_file
def prepare_exclude_file(items, base_file, chrom=None):
"""Prepare a BED file for exclusion.
Excludes high depth and centromere regions which contribute to long run times and
false positive structural variant calls.
"""
items = shared.add_highdepth_genome_exclusion(items)
out_file = "%s-exclude%s.bed" % (utils.splitext_plus(base_file)[0], "-%s" % chrom if chrom else "")
if not utils.file_exists(out_file) and not utils.file_exists(out_file + ".gz"):
with shared.bedtools_tmpdir(items[0]):
with file_transaction(items[0], out_file) as tx_out_file:
# Get a bedtool for the full region if no variant regions
want_bedtool = callable.get_ref_bedtool(tz.get_in(["reference", "fasta", "base"], items[0]),
items[0]["config"], chrom)
want_bedtool = pybedtools.BedTool(shared.subset_variant_regions(want_bedtool.saveas().fn,
chrom, tx_out_file, items))
sv_exclude_bed = _get_sv_exclude_file(items)
if sv_exclude_bed and len(want_bedtool) > 0:
want_bedtool = want_bedtool.subtract(sv_exclude_bed, nonamecheck=True).saveas()
full_bedtool = callable.get_ref_bedtool(tz.get_in(["reference", "fasta", "base"], items[0]),
items[0]["config"])
if len(want_bedtool) > 0:
full_bedtool.subtract(want_bedtool, nonamecheck=True).saveas(tx_out_file)
else:
full_bedtool.saveas(tx_out_file)
return out_file
def run_freebayes(align_bams,
items,
ref_file,
assoc_files,
region=None,
out_file=None):
"""Run FreeBayes variant calling, either paired tumor/normal or germline calling.
"""
items = shared.add_highdepth_genome_exclusion(items)
if is_paired_analysis(align_bams, items):
paired = get_paired_bams(align_bams, items)
if not paired.normal_bam:
call_file = _run_freebayes_caller(align_bams,
items,
ref_file,
assoc_files,
region,
out_file,
somatic=paired)
else:
call_file = _run_freebayes_paired(
[paired.tumor_bam, paired.normal_bam],
[paired.tumor_data, paired.normal_data], ref_file, assoc_files,
region, out_file)
else:
vcfutils.check_paired_problems(items)
call_file = _run_freebayes_caller(align_bams, items, ref_file,
assoc_files, region, out_file)
return call_file
def run_vardict(align_bams, items, ref_file, assoc_files, region=None,
out_file=None):
"""Run VarDict variant calling.
"""
items = shared.add_highdepth_genome_exclusion(items)
if vcfutils.is_paired_analysis(align_bams, items):
call_file = _run_vardict_paired(align_bams, items, ref_file,
assoc_files, region, out_file)
else:
vcfutils.check_paired_problems(items)
call_file = _run_vardict_caller(align_bams, items, ref_file,
assoc_files, region, out_file)
return call_file
def run_freebayes(align_bams, items, ref_file, assoc_files, region=None,
out_file=None):
"""Run FreeBayes variant calling, either paired tumor/normal or germline calling.
"""
items = shared.add_highdepth_genome_exclusion(items)
if is_paired_analysis(align_bams, items):
paired = get_paired_bams(align_bams, items)
if not paired.normal_bam:
call_file = _run_freebayes_caller(align_bams, items, ref_file,
assoc_files, region, out_file, somatic=paired)
else:
call_file = _run_freebayes_paired([paired.tumor_bam, paired.normal_bam],
[paired.tumor_data, paired.normal_data],
ref_file, assoc_files, region, out_file)
else:
vcfutils.check_paired_problems(items)
call_file = _run_freebayes_caller(align_bams, items, ref_file,
assoc_files, region, out_file)
return call_file
