Thanks to Michael and Julian for taking care of this. Fixes are in
devel, >= 1.13.15.
Valerie
On 12/03/14 08:44, Michael Lawrence wrote:
Looks like an issue when expand()ing the VCF. Maybe Val could take a look?
On Wed, Dec 3, 2014 at 7:39 AM, Julian Gehring <julian.gehring at embl.de>
wrote:
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