[Bioc-devel] VariantAnnotation: VCF to VRanges with multiple INFO values

Julian Gehring julian.gehring at embl.de
Wed Dec 3 16:39:41 CET 2014


The conversion from a 'VCF' to 'VRanges' object fails if an INFO field
with multiple values for different ALT alleles is present:

Here an example VCF entry for which this fails (line 71151250 in
, taken from

  10001541	rs12451372	C	G,T	100	PASS

The respective code to reproduce this:

  roi = GRanges("17", IRanges(1e7+1541, width = 1))
  vcf = readVcf(path, "GRCh37", ScanVcfParam(which = roi, info = "AF"))
  ## 'info = character()' and other versions also cause the error

  vrc = as(vcf, "VRanges") ## error

fails with

  Error in colSums(ielt) : 'x' must be an array of at least two dimensions

This occurs both with the latest version of VariantAnnotation in
bioc-release and bioc-devel.


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