def run_haplotyper(align_bams,
items,
ref_file,
assoc_files,
region=None,
out_file=None):
"""Call variants with Sentieon's haplotyper (GATK HaplotypeCaller like).
"""
if out_file is None:
out_file = "%s-variants.vcf.gz" % utils.splitext_plus(align_bams[0])[0]
if not utils.file_exists(out_file):
variant_regions = bedutils.merge_overlaps(
dd.get_variant_regions(items[0]), items[0])
interval = _get_interval(variant_regions, region, out_file, items)
with file_transaction(items[0], out_file) as tx_out_file:
dbsnp = "--dbsnp %s" % (
assoc_files.get("dbsnp")) if "dbsnp" in assoc_files else ""
bams = " ".join(["-i %s" % x for x in align_bams])
license = license_export(items[0])
cores = dd.get_num_cores(items[0])
out_mode = "--emit_mode gvcf" if joint.want_gvcf(items) else ""
cmd = (
"{license}sentieon driver -t {cores} -r {ref_file} "
"{bams} {interval} --algo Haplotyper {out_mode} {dbsnp} {tx_out_file}"
)
do.run(cmd.format(**locals()), "Sentieon Haplotyper")
return out_file
def _run_germline(align_bams, items, ref_file, assoc_files, region, out_file):
if not utils.file_exists(out_file):
work_dir = "%s-work" % utils.splitext_plus(out_file)[0]
with file_transaction(items[0], work_dir) as tx_work_dir:
workflow_file = _configure_germline(align_bams, items, ref_file, region, out_file, tx_work_dir)
_run_workflow(items[0], workflow_file, tx_work_dir)
raw_file = os.path.join(work_dir, "results", "variants",
"genome.vcf.gz" if joint.want_gvcf(items) else "variants.vcf.gz")
utils.symlink_plus(raw_file, out_file)
return vcfutils.bgzip_and_index(out_file, items[0]["config"])
def _run_germline(align_bams, items, ref_file, assoc_files, region, out_file, work_dir):
if not utils.file_exists(out_file):
with file_transaction(items[0], work_dir) as tx_work_dir:
workflow_file = _configure_germline(align_bams, items, ref_file, region, out_file, tx_work_dir)
_run_workflow(items[0], workflow_file, tx_work_dir)
raw_file = os.path.join(work_dir, "results", "variants",
"genome.vcf.gz" if joint.want_gvcf(items) else "variants.vcf.gz")
utils.copy_plus(raw_file, out_file)
# Remove files with relative symlinks
utils.remove_plus(os.path.join(work_dir, "results", "variants", "genome.vcf.gz"))
return vcfutils.bgzip_and_index(out_file, items[0]["config"])
def _run_germline(align_bams, items, ref_file, assoc_files, region, out_file, work_dir):
if not utils.file_exists(out_file):
with file_transaction(items[0], work_dir) as tx_work_dir:
workflow_file = _configure_germline(align_bams, items, ref_file, region, out_file, tx_work_dir)
_run_workflow(items[0], workflow_file, tx_work_dir)
raw_file = os.path.join(work_dir, "results", "variants",
"genome.vcf.gz" if joint.want_gvcf(items) else "variants.vcf.gz")
utils.copy_plus(raw_file, out_file)
# Remove files with relative symlinks
utils.remove_plus(os.path.join(work_dir, "results", "variants", "genome.vcf.gz"))
return vcfutils.bgzip_and_index(out_file, items[0]["config"])
def _run_germline(align_bams, items, ref_file, assoc_files, region, out_file):
if not utils.file_exists(out_file):
work_dir = "%s-work" % utils.splitext_plus(out_file)[0]
with file_transaction(items[0], work_dir) as tx_work_dir:
workflow_file = _configure_germline(align_bams, items, ref_file, region, out_file, tx_work_dir)
_run_workflow(items[0], workflow_file, tx_work_dir)
raw_file = os.path.join(work_dir, "results", "variants",
"genome.vcf.gz" if joint.want_gvcf(items) else "variants.vcf.gz")
out_file = annotation.annotate_nongatk_vcf(raw_file, align_bams, assoc_files.get("dbsnp"),
ref_file, items[0], out_file)
return vcfutils.bgzip_and_index(out_file, items[0]["config"])
def run_haplotyper(align_bams, items, ref_file, assoc_files,
region=None, out_file=None):
"""Call variants with Sentieon's haplotyper (GATK HaplotypeCaller like).
"""
if out_file is None:
out_file = "%s-variants.vcf.gz" % utils.splitext_plus(align_bams[0])[0]
if not utils.file_exists(out_file):
variant_regions = bedutils.merge_overlaps(dd.get_variant_regions(items[0]), items[0])
interval = _get_interval(variant_regions, region, out_file, items)
with file_transaction(items[0], out_file) as tx_out_file:
dbsnp = "--dbsnp %s" % (assoc_files.get("dbsnp")) if "dbsnp" in assoc_files else ""
bams = " ".join(["-i %s" % x for x in align_bams])
license = license_export(items[0])
cores = dd.get_num_cores(items[0])
out_mode = "--emit_mode gvcf" if joint.want_gvcf(items) else ""
cmd = ("{license}sentieon driver -t {cores} -r {ref_file} "
"{bams} {interval} --algo Haplotyper {out_mode} {dbsnp} {tx_out_file}")
do.run(cmd.format(**locals()), "Sentieon Haplotyper")
return out_file
def _run_germline(align_bams, items, ref_file, assoc_files, region, out_file,
work_dir):
if not utils.file_exists(out_file):
with file_transaction(items[0], work_dir) as tx_work_dir:
workflow_file = _configure_germline(align_bams, items, ref_file,
region, out_file, tx_work_dir)
if workflow_file:
has_variants = True
_run_workflow(items[0], workflow_file, tx_work_dir)
else:
has_variants = False
vcfutils.write_empty_vcf(
out_file, items[0]["config"],
[dd.get_sample_name(d) for d in items])
if has_variants:
raw_file = os.path.join(
work_dir, "results", "variants", "genome.vcf.gz"
if joint.want_gvcf(items) else "variants.vcf.gz")
utils.copy_plus(raw_file, out_file)
# Remove files with relative symlinks
utils.remove_plus(
os.path.join(work_dir, "results", "variants", "genome.vcf.gz"))
return vcfutils.bgzip_and_index(out_file, items[0]["config"])
