def calculate_sv_coverage(data):
"""Calculate coverage within bins for downstream CNV calling.
Creates corrected cnr files with log2 ratios and depths.
"""
from bcbio.variation import coverage
from bcbio.structural import annotate, cnvkit
data = utils.to_single_data(data)
if not cnvkit.use_general_sv_bins(data):
return [[data]]
work_dir = utils.safe_makedir(os.path.join(dd.get_work_dir(data), "structural",
dd.get_sample_name(data), "bins"))
out_target_file = os.path.join(work_dir, "%s-target-coverage.cnn" % dd.get_sample_name(data))
out_anti_file = os.path.join(work_dir, "%s-antitarget-coverage.cnn" % dd.get_sample_name(data))
if ((not utils.file_exists(out_target_file) or not utils.file_exists(out_anti_file))
and (dd.get_align_bam(data) or dd.get_work_bam(data))):
# mosdepth
target_cov = coverage.run_mosdepth(data, "target", tz.get_in(["regions", "bins", "target"], data))
anti_cov = coverage.run_mosdepth(data, "antitarget", tz.get_in(["regions", "bins", "antitarget"], data))
target_cov_genes = annotate.add_genes(target_cov.regions, data, max_distance=0)
anti_cov_genes = annotate.add_genes(anti_cov.regions, data, max_distance=0)
out_target_file = _add_log2_depth(target_cov_genes, out_target_file, data)
out_anti_file = _add_log2_depth(anti_cov_genes, out_anti_file, data)
# TODO: Correct for GC bias
if os.path.exists(out_target_file):
data["depth"]["bins"] = {"target": out_target_file, "antitarget": out_anti_file}
return [[data]]
def _calculate_sv_coverage_cnvkit(data, work_dir):
"""Calculate coverage in an CNVkit ready format using mosdepth.
"""
from bcbio.variation import coverage
from bcbio.structural import annotate
out_target_file = os.path.join(
work_dir, "%s-target-coverage.cnn" % dd.get_sample_name(data))
out_anti_file = os.path.join(
work_dir, "%s-antitarget-coverage.cnn" % dd.get_sample_name(data))
if ((not utils.file_exists(out_target_file)
or not utils.file_exists(out_anti_file))
and (dd.get_align_bam(data) or dd.get_work_bam(data))):
target_cov = coverage.run_mosdepth(
data, "target", tz.get_in(["regions", "bins", "target"], data))
anti_cov = coverage.run_mosdepth(
data, "antitarget",
tz.get_in(["regions", "bins", "antitarget"], data))
target_cov_genes = annotate.add_genes(target_cov.regions,
data,
max_distance=0)
anti_cov_genes = annotate.add_genes(anti_cov.regions,
data,
max_distance=0)
out_target_file = _add_log2_depth(target_cov_genes, out_target_file,
data)
out_anti_file = _add_log2_depth(anti_cov_genes, out_anti_file, data)
return out_target_file, out_anti_file
def _calculate_sv_coverage_cnvkit(data, work_dir):
"""Calculate coverage in an CNVkit ready format using mosdepth.
"""
from bcbio.variation import coverage
from bcbio.structural import annotate
out_target_file = os.path.join(work_dir, "%s-target-coverage.cnn" % dd.get_sample_name(data))
out_anti_file = os.path.join(work_dir, "%s-antitarget-coverage.cnn" % dd.get_sample_name(data))
if ((not utils.file_exists(out_target_file) or not utils.file_exists(out_anti_file)) and
(dd.get_align_bam(data) or dd.get_work_bam(data))):
target_cov = coverage.run_mosdepth(data, "target", tz.get_in(["regions", "bins", "target"], data))
anti_cov = coverage.run_mosdepth(data, "antitarget", tz.get_in(["regions", "bins", "antitarget"], data))
target_cov_genes = annotate.add_genes(target_cov.regions, data, max_distance=0)
out_target_file = _add_log2_depth(target_cov_genes, out_target_file, data)
out_anti_file = _add_log2_depth(anti_cov.regions, out_anti_file, data)
return out_target_file, out_anti_file
def _calculate_sv_coverage_gatk(data, work_dir):
"""Calculate coverage in defined regions using GATK tools
TODO: This does double calculations to get GATK4 compatible HDF read counts
and then depth and gene annotations. Both are needed for creating heterogeneity inputs.
Ideally replace with a single mosdepth coverage calculation, and creat GATK4 TSV format:
CONTIG START END COUNT
chrM 1 1000 13268
"""
from bcbio.variation import coverage
from bcbio.structural import annotate
# GATK compatible
target_file = gatkcnv.collect_read_counts(data, work_dir)
# heterogeneity compatible
target_in = bedutils.clean_file(tz.get_in(["regions", "bins", "target"], data), data, bedprep_dir=work_dir)
target_cov = coverage.run_mosdepth(data, "target-gatk", target_in)
target_cov_genes = annotate.add_genes(target_cov.regions, data, max_distance=0)
return target_file, target_cov_genes
def _calculate_sv_coverage_gatk(data, work_dir):
"""Calculate coverage in defined regions using GATK tools
TODO: This does double calculations to get GATK4 compatible HDF read counts
and then depth and gene annotations. Both are needed for creating heterogeneity inputs.
Ideally replace with a single mosdepth coverage calculation, and creat GATK4 TSV format:
CONTIG START END COUNT
chrM 1 1000 13268
"""
from bcbio.variation import coverage
from bcbio.structural import annotate
# GATK compatible
target_file = gatkcnv.collect_read_counts(data, work_dir)
# heterogeneity compatible
target_in = bedutils.clean_file(tz.get_in(["regions", "bins", "target"], data), data, bedprep_dir=work_dir)
target_cov = coverage.run_mosdepth(data, "target-gatk", target_in)
target_cov_genes = annotate.add_genes(target_cov.regions, data, max_distance=0)
return target_file, target_cov_genes
