Hi,

By running

(vcf <- readVcf(vcffile, "hg38"))

in VariantAnnotation I get an error message

Error in DataFrame(Samples = seq_along(colnms), row.names = colnms) : duplicate row names

What may be causing this? I am not sure how I ended up with duplicate

names in the VCF file. My VCF file was generated by merging several

files using vcftools  vcf-merge function. May this be the problem?

Thank you!

>sessionInfo()
R version 3.1.1 (2014-07-10)
Platform: x86_64-w64-mingw32/x64 (64-bit)

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252 LC_NUMERIC=C                          
[5] LC_TIME=English_United States.1252    

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

other attached packages:
 [1] VariantAnnotation_1.12.2 Rsamtools_1.18.1         Biostrings_2.34.0        XVector_0.6.0            GenomicRanges_1.18.1     GenomeInfoDb_1.2.2      
 [7] IRanges_2.0.0            S4Vectors_0.4.0          GWASTools_1.12.0         gdsfmt_1.0.4             ncdf_1.6.8               Biobase_2.26.0          
[13] BiocGenerics_0.12.0     

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.28.1    base64enc_0.1-2         BatchJobs_1.4           BBmisc_1.7              BiocParallel_1.0.0      biomaRt_2.22.0         
 [7] bitops_1.0-6            brew_1.0-6              BSgenome_1.34.0         checkmate_1.4           codetools_0.2-9         DBI_0.3.1              
[13] digest_0.6.4            DNAcopy_1.40.0          fail_1.2                foreach_1.4.2           GenomicAlignments_1.2.0 GenomicFeatures_1.18.2 
[19] grid_3.1.1              GWASExactHW_1.01        iterators_1.0.7         lattice_0.20-29         lmtest_0.9-33           quantreg_5.05          
[25] quantsmooth_1.32.0      RCurl_1.95-4.3          RSQLite_0.11.4          rtracklayer_1.26.1      sandwich_2.3-2          sendmailR_1.2-1        
[31] SparseM_1.05            splines_3.1.1           stringr_0.6.2           survival_2.37-7         tools_3.1.1             XML_3.98-1.1           
[37] zlibbioc_1.12.0         zoo_1.7-11             

Hi Jozsef,

The duplicate names are likely in the header FORMAT fields. If the file isn't too big, open it in an editor and look at the header tags marked with FORMAT. According to the vcf spec, the 'ID' key for a particular field should be unique. This means lines starting with INFO should have different 'ID' keys, the same applies for lines starting with FORMAT.

You can try reading in just the header information but if you have duplicate fields you may get an error:

> fl <- system.file("extdata", "ex2.vcf", package="VariantAnnotation")
> hdr <- scanVcfHeader(fl)

Another approach is to scan in the data then look at the names of the FORMAT (i.e., 'geno') fields:

> scn <- scanVcf(fl)
> names(scn[[1]]$GENO)
[1] "GT" "GQ" "DP" "HQ"

Valerie