def run(items):
"""Run MetaSV if we have enough supported callers, adding output to the set of calls.
"""
assert len(items) == 1, "Expect one input to MetaSV ensemble calling"
data = items[0]
work_dir = _sv_workdir(data)
out_file = os.path.join(work_dir, "variants.vcf.gz")
cmd = _get_cmd() + ["--sample", dd.get_sample_name(data), "--reference", dd.get_ref_file(data),
"--bam", dd.get_align_bam(data), "--outdir", work_dir]
methods = []
for call in data.get("sv", []):
if call["variantcaller"] in SUPPORTED and call["variantcaller"] not in methods:
methods.append(call["variantcaller"])
cmd += ["--%s_vcf" % call["variantcaller"], call.get("vcf_file", call["vrn_file"])]
if len(methods) >= MIN_CALLERS:
if not utils.file_exists(out_file):
tx_work_dir = utils.safe_makedir(os.path.join(work_dir, "raw"))
ins_stats = shared.calc_paired_insert_stats_save(dd.get_align_bam(data),
os.path.join(tx_work_dir, "insert-stats.yaml"))
cmd += ["--workdir", tx_work_dir, "--num_threads", str(dd.get_num_cores(data))]
cmd += ["--spades", utils.which("spades.py"), "--age", utils.which("age_align")]
cmd += ["--assembly_max_tools=1", "--assembly_pad=500"]
cmd += ["--boost_sc", "--isize_mean", ins_stats["mean"], "--isize_sd", ins_stats["std"]]
do.run(cmd, "Combine variant calls with MetaSV")
filters = ("(NUM_SVTOOLS = 1 && ABS(SVLEN)>50000) || "
"(NUM_SVTOOLS = 1 && ABS(SVLEN)<4000 && BA_FLANK_PERCENT>80) || "
"(NUM_SVTOOLS = 1 && ABS(SVLEN)<4000 && BA_NUM_GOOD_REC=0) || "
"(ABS(SVLEN)<4000 && BA_NUM_GOOD_REC>2)")
filter_file = vfilter.cutoff_w_expression(out_file, filters,
data, name="ReassemblyStats", limit_regions=None)
effects_vcf, _ = effects.add_to_vcf(filter_file, data, "snpeff")
data["sv"].append({"variantcaller": "metasv",
"vrn_file": effects_vcf or filter_file})
return [data]
def _filter_by_support(in_file, data):
"""Filter call file based on supporting evidence, adding FILTER annotations to VCF.
Filters based on the following criteria:
- Minimum read support for the call (SU = total support)
- Large calls need split read evidence.
"""
rc_filter = ("FORMAT/SU < 4 || "
"(FORMAT/SR == 0 && FORMAT/SU < 15 && ABS(SVLEN)>50000) || "
"(FORMAT/SR == 0 && FORMAT/SU < 5 && ABS(SVLEN)<2000) || "
"(FORMAT/SR == 0 && FORMAT/SU < 15 && ABS(SVLEN)<300)")
return vfilter.cutoff_w_expression(in_file, rc_filter, data, name="ReadCountSupport",
limit_regions=None)
def _filter_by_support(in_file, data):
"""Filter call file based on supporting evidence, adding FILTER annotations to VCF.
Filters based on the following criteria:
- Minimum read support for the call (SU = total support)
- Large calls need split read evidence.
"""
rc_filter = ("FORMAT/SU < 4 || "
"(FORMAT/SR == 0 && FORMAT/SU < 15 && ABS(SVLEN)>50000) || "
"(FORMAT/SR == 0 && FORMAT/SU < 5 && ABS(SVLEN)<2000) || "
"(FORMAT/SR == 0 && FORMAT/SU < 15 && ABS(SVLEN)<300)")
return vfilter.cutoff_w_expression(in_file, rc_filter, data, name="ReadCountSupport",
limit_regions=None)
