def _calculate_sv_bins_gatk(data, cnv_group, size_calc_fn):
"""Calculate structural variant bins using GATK4 CNV callers region or even intervals approach.
"""
target_bed = gatkcnv.prepare_intervals(data, cnv_group.region_file,
cnv_group.work_dir)
gc_annotated_tsv = gatkcnv.annotate_intervals(target_bed, data)
return target_bed, None, gc_annotated_tsv
def _calculate_sv_bins_gatk(data, cnv_group, size_calc_fn):
"""Calculate structural variant bins using GATK4 CNV callers region or even intervals approach.
"""
if dd.get_background_cnv_reference(data, "gatk-cnv"):
target_bed = gatkcnv.pon_to_bed(dd.get_background_cnv_reference(data, "gatk-cnv"), cnv_group.work_dir, data)
else:
target_bed = gatkcnv.prepare_intervals(data, cnv_group.region_file, cnv_group.work_dir)
gc_annotated_tsv = gatkcnv.annotate_intervals(target_bed, data)
return target_bed, None, gc_annotated_tsv
def _calculate_sv_bins_gatk(data, cnv_group, size_calc_fn):
"""Calculate structural variant bins using GATK4 CNV callers region or even intervals approach.
"""
if dd.get_background_cnv_reference(data, "gatk-cnv"):
target_bed = gatkcnv.pon_to_bed(dd.get_background_cnv_reference(data, "gatk-cnv"), cnv_group.work_dir, data)
else:
target_bed = gatkcnv.prepare_intervals(data, cnv_group.region_file, cnv_group.work_dir)
gc_annotated_tsv = gatkcnv.annotate_intervals(target_bed, data)
return target_bed, None, gc_annotated_tsv