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flag to address bcftools merge chopping
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Melissa Gymrek authored and Melissa Gymrek committed Aug 31, 2024
1 parent c77fecc commit b0b0b38
Showing 1 changed file with 1 addition and 1 deletion.
2 changes: 1 addition & 1 deletion trtools/annotaTR/annotaTR.py
Original file line number Diff line number Diff line change
Expand Up @@ -567,7 +567,7 @@ def main(args):
for infofield in INFOFIELDS[vcftype]:
record.INFO[infofield] = refpanel_metadata[locuskey][infofield]
if args.fix_bcftools_offset:
refoffset = len(record.REF)-len(refpanel_metadata[locuskey]["REF"])
refoffset = len(refpanel_metadata[locuskey]["REF"])-len(record.REF)
try:
trrecord = trh.HarmonizeRecord(vcfrecord=record, vcftype=vcftype, ref_offset=refoffset)
except:
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