Hello,
I am currently playing with edit operations on genomic sequences and I have
to following problem. Imagine that you have a FASTA reference and you have
editated it. How to save these edit operations? With respect to existing
tools, the format VCF seems to be the most natural (even though it is not
intended for it).
My questions are:
Q1: Do you know about any better standard format than VCF for this purpose?
Q2: Do you have any idea about some existing program converting VCF to
chain files (for recomputing coordinates in, e.g., SAM files)?
Q2.1: Is there any support in "bcftools consensus" for chain files (in the
output)?
Q3: Do you know about any tool which can make a composition of two or more
VCF files (and also of two chain files)? The difficulty is that such tool
must be aware of indels in the first file.
Why I am writing this question here:
- I believe that this functionality should be supported by BCF tools
(chain file as an output of "bcftools consensus", etc.).
- If it does not exist yet, it would be nice to have a standard way how
to save edit operations on genomes (a subset of VCF would perfectly suit --
similarly to PDF and its subsets like PDF/A). I remember from few papers
that some people use VCF for saving differences between genomes but other
people still consider it to be a crazy idea (see, e.g.,
http://www.biostars.org/p/98445/).
Thanks
Karel Brinda
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