Hi. I've started using the "VariantAnnotation" package for loading a vcf into R using readVcf. Seems to work well, and I like the functionality so far. However, I noticed that if I use a vcf that has been previously annotated with Snpsift using dbnsfp, I get an error:

Error in x[[i]] : subscript out of bounds

The following is my code:

library("VariantAnnotation")
tabfile <- TabixFile("test.dbsnfp.vcf.gz", yieldSize=50)
open(tabfile)
vcf3 <- readVcf(tabfile, "hg19")
close(tabfile)​

If using the same vcf file, but just before annotating with dbnsfp, I do not get the error and the vcf loads.

I can provide example files if interested. Wondering if anybody else has encountered this problem.

Thanks, 

Jason

> sessionInfo()
R version 3.1.2 (2014-10-31)
Platform: x86_64-apple-darwin13.4.0 (64-bit)

locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] VariantAnnotation_1.12.9 Rsamtools_1.18.2         Biostrings_2.34.0        XVector_0.6.0           
 [5] GenomicRanges_1.18.3     GenomeInfoDb_1.2.3       IRanges_2.0.1            S4Vectors_0.4.0         
 [9] BiocGenerics_0.12.1      stringr_0.6.2           

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.28.1    base64enc_0.1-2         BatchJobs_1.5           BBmisc_1.8             
 [5] Biobase_2.26.0          BiocParallel_1.0.0      biomaRt_2.22.0          bitops_1.0-6           
 [9] brew_1.0-6              BSgenome_1.34.1         checkmate_1.5.0         codetools_0.2-9        
[13] colorspace_1.2-4        DBI_0.3.1               digest_0.6.4            fail_1.2               
[17] foreach_1.4.2           GenomicAlignments_1.2.1 GenomicFeatures_1.18.2  ggplot2_1.0.0          
[21] grid_3.1.2              gtable_0.1.2            iterators_1.0.7         MASS_7.3-35            
[25] munsell_0.4.2           plyr_1.8.1              proto_0.3-10            Rcpp_0.11.3            
[29] RCurl_1.95-4.3          reshape2_1.4            RSQLite_1.0.0           rtracklayer_1.26.2     
[33] scales_0.2.4            sendmailR_1.2-1         tools_3.1.2             XML_3.98-1.1           
[37] zlibbioc_1.12.0 

Hi,

In the SnpSift docs I don't see an example of how the dpnsfp command annotates the file. Are the new fields added to INFO? You may want to look a the first few lines of the file to see what what done.

I can take a look at the file if you provide it offline (vobencha@fredhutch.org). readVcf() expects a vcf file that adheres, for the most part, to the specs. If there are reasonable deviations we try to support that.

Valerie

Thank you Valerie. Just send you some VCF files that should reproduce the problem on your end.

Jason