This turns out to be hard to do because rover does not require the reference sequence to be present. We don't necessarily know the base just prior to the start of the read for example.
It looks like Annovar wants its input in this format because of the way VCF is defined.
However it seems like the "Annovar" input (not VCF) doesn't have this requirement, so maybe we can make annovar friendly files as an optional output instead?
bjpop
commented
10 years ago
This turns out to be hard to do because rover does not require the reference sequence to be present. We don't necessarily know the base just prior to the start of the read for example.
It looks like Annovar wants its input in this format because of the way VCF is defined.
However it seems like the "Annovar" input (not VCF) doesn't have this requirement, so maybe we can make annovar friendly files as an optional output instead?