Question: AllelicImbalance with VCFs?
5.6 years ago by
Tim Triche, Jr. • 10
Tim Triche, Jr. • 10 wrote:
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 [[alternative HTML version deleted]]
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