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Commit fbd1bc81 authored by Wai Yi Leung's avatar Wai Yi Leung
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by default report the SVtype in the ALT field

parent 9ae3e5c2
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biopet-extensions/src/main/resources/nl/lumc/sasc/biopet/extensions/breakdancer/breakdancer2vcf.py
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...@@ -157,7 +157,7 @@ def _format_vcffile(dictreader, vcffile, samplename): ...@@ -157,7 +157,7 @@ def _format_vcffile(dictreader, vcffile, samplename):
CHROM = line['Chr1'] CHROM = line['Chr1']
# TODO Figure out whether we have zero or one based positioning # TODO Figure out whether we have zero or one based positioning
POS = int(line['Pos1']) POS = int(line['Pos1'])
ALT = '.' ALT = '<{}>'.format(line['Type'])
SVEND = int(line['Pos2']) SVEND = int(line['Pos2'])
INFO = 'SVMETHOD=breakdancer;SVTYPE={}'.format(line['Type']) INFO = 'SVMETHOD=breakdancer;SVTYPE={}'.format(line['Type'])
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