vcf2maf
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Infer Frame from breakend format for SVs
VCF specs define the breakend format as follows:
REF ALT Meaning
s t[p[ piece extending to the right of p is joined after t
s t]p] reverse comp piece extending left of p is joined after t
s ]p]t piece extending to the left of p is joined before t
s [p[t reverse comp piece extending right of p is joined before t
This should map to Frame
info as follows:
t[p[ 5to3
t]p] 3to3
]p]t 3to5
[p[t 5to5