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Add GT format field #4

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Add GT format field #4

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12 changes: 10 additions & 2 deletions bin/mergeVCFCallers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -40,8 +40,10 @@ def getNewHeaderAttr(args):
final_format = {
"AD": HeaderFormatAttr("AD", type="Integer", number="A", description="Allele Depth"),
"DP": HeaderFormatAttr("DP", type="Integer", number="1", description="Total Depth"),
"GT": HeaderFormatAttr("GT", type="String", number="1", description="Genotype"),
"ADSRC": HeaderFormatAttr("ADSRC", type="Integer", number=".", description="Allele Depth by source"),
"DPSRC": HeaderFormatAttr("DPSRC", type="Integer", number=".", description="Total Depth by source")
"DPSRC": HeaderFormatAttr("DPSRC", type="Integer", number=".", description="Total Depth by source"),
"GTSRC": HeaderFormatAttr("GTSRC", type="String", number=".", description="Genotype by source")
}
final_samples = None
for idx_in, curr_in in enumerate(args.inputs_variants):
Expand Down Expand Up @@ -119,7 +121,8 @@ def getMergedRecords(inputs_variants, calling_sources, annotations_field, shared
for spl in FH_in.samples:
support_by_spl[spl] = {
"AD": record.getAltAD(spl)[0],
"DP": record.getDP(spl)
"DP": record.getDP(spl),
"GT": record.getGT(spl)
}
# Rename filters
if record.filter is not None:
Expand Down Expand Up @@ -160,13 +163,17 @@ def getMergedRecords(inputs_variants, calling_sources, annotations_field, shared
# AD and DP by sample (from the first caller finding the variant: callers are in user order)
record.format.insert(0, "ADSRC")
record.format.insert(0, "DPSRC")
record.format.insert(0, "GTSRC")
record.format.insert(0, "AD")
record.format.insert(0, "DP")
record.format.insert(0, "GT")
for spl_name, spl_data in record.samples.items():
spl_data["AD"] = [support_by_spl[spl_name]["AD"]]
spl_data["DP"] = support_by_spl[spl_name]["DP"]
spl_data["GT"] = support_by_spl[spl_name]["GT"]
spl_data["ADSRC"] = [support_by_spl[spl_name]["AD"]]
spl_data["DPSRC"] = [support_by_spl[spl_name]["DP"]]
spl_data["GTSRC"] = [support_by_spl[spl_name]["GT"]]
else:
prev_variant = variant_by_name[variant_name]
prev_variant.info["SRC"].append(curr_caller)
Expand All @@ -190,6 +197,7 @@ def getMergedRecords(inputs_variants, calling_sources, annotations_field, shared
spl_data.update(record.samples[spl_name])
spl_data["ADSRC"].append(support_by_spl[spl_name]["AD"])
spl_data["DPSRC"].append(support_by_spl[spl_name]["DP"])
spl_data["GTSRC"].append(support_by_spl[spl_name]["GT"])
return variant_by_name.values()


Expand Down