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Provide a bait file to Picard's CollectHsMetrics #3695

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Provide a bait file to Picard's CollectHsMetrics #3695

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2c492fd
Add ``bait_regions`` to data_dict
asee-imagia Jan 27, 2023
c35fd5a
Provide a bait file to picard's CollectHsMetrics
asee-imagia Jan 27, 2023
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1 change: 1 addition & 0 deletions bcbio/pipeline/datadict.py
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Original file line number Diff line number Diff line change
Expand Up @@ -166,6 +166,7 @@
"vrn_file": {"keys": ["vrn_file"]},
"exclude_regions": {"keys": ["config", "algorithm", "exclude_regions"], "default": [],
"always_list": True},
"bait_regions": {"keys": ["config", "algorithm", "bait_regions"]},
"variant_regions": {"keys": ["config", "algorithm", "variant_regions"]},
"variant_regions_merged": {"keys": ["config", "algorithm", "variant_regions_merged"]},
"variant_regions_orig": {"keys": ["config", "algorithm", "variant_regions_orig"]},
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3 changes: 2 additions & 1 deletion bcbio/qc/picard.py
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Expand Up @@ -14,6 +14,7 @@ def run(bam_file, data, out_dir):
ref_file = dd.get_ref_file(data)
sample = dd.get_sample_name(data)
target_file = dd.get_variant_regions(data) or dd.get_sample_callable(data)
bait_file = dd.get_bait_regions(data) or target_file
broad_runner = broad.PicardCmdRunner("picard", data["config"])
bam_fname = os.path.abspath(bam_file)
path = os.path.dirname(bam_fname)
Expand All @@ -30,7 +31,7 @@ def run(bam_file, data, out_dir):
gen_metrics = PicardMetrics(broad_runner, tmp_dir)
gen_metrics.report(cur_bam, ref_file,
bam.is_paired(bam_fname),
target_file, target_file, None, data["config"])
bait_file, target_file, None, data["config"])
if utils.file_exists(hsmetric_file):
do.run("sed -i 's/%s.bam//g' %s" % (out_base.replace(sample, ""), hsmetric_file), "")
if utils.file_exists(hsinsert_file):
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