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.gehr...@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 > > _______________________________________________ > Bioc-devel@r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/bioc-devel > [[alternative HTML version deleted]] _______________________________________________ Bioc-devel@r-project.org mailing list https://stat.ethz.ch/mailman/listinfo/bioc-devel
