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

[Julian Gehring]

Hi,

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
'ALL.wgs.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.vcf.gz'
, taken from
ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5.20130502.sites.vcf.gz):

  10001541	rs12451372	C	G,T	100	PASS
  AC=700,298;AF=0.139776,0.0595048;AN=5008;NS=2504;DP=17289;EAS_AF=0.2421,0;AMR_AF=0.1801,0.0115;AFR_AF=0.0749,0.2194;EUR_AF=0.0915,0;SAS_AF=0.1431,0;AA=T|||

The respective code to reproduce this:

  library(VariantAnnotation)
  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.

Best
Julian