Hi all,

I'm looking to verify some RNAseq results using (in some cases phased) SNP
calls from the CEU trio and from primary samples in-house (case and matched
control).  AllelicImbalance looks like a terrific library for this, however
my BCFs can't be read by Rsamtools::scanBcf.  (I get an error "Error:
scanBcf: failed to find fmt encoded as '16977'  path:
/scratch/BAMs/LIU1675A8.hg19.bcf")

VariantAnnotation::scanVcf, on the other hand, works fine.

So, is there any particular reason why I couldn't hack up
the impBcfGL/impBcfGRL method to use VCFs?  Also, would it make sense to
have a default argument for searchArea that falls back to the assembly in
the metadata, if one is specified?

The bizarre thing with the BCFs is that I can scan their headers just
fine... !

Thanks,

Timothy J. Triche, Jr., PhD
Jane Anne Nohl Division of Hematology
USC/Norris Comprehensive Cancer Center

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