Hi all, I am reading in some .vcf files with the readVcf function and realized that I cannot subset the resulting VCF objects if the info field is empty, see example below. Is there a workaround except for loading the info at least partially? Thanks, Paul The Example: > vcf_full = readVcf("test.vcf.gz", "hg19") > vcf_no_info = readVcf("test.vcf.gz", "hg19", param = ScanVcfParam( geno=c("GT","GQ"), fixed="ALT", info=NA )) vcf_full class: VCF dim: 71128 2 genome: hg19 exptData(1): header fixed(4): REF ALT QUAL FILTER info(22): AC AF ... SB STR geno(5): AD DP GQ GT PL rownames(71128): rs62224610 rs141578542 ... 22:51243743 22:51244332 rowData values names(1): paramRangeID colnames(2): sample_one sample_two colData names(1): Samples > vcf_no_info class: VCF dim: 71128 2 genome: hg19 exptData(1): header fixed(2): REF ALT info(0): geno(2): GQ GT rownames(71128): rs62224610 rs141578542 ... 22:51243743 22:51244332 rowData values names(1): paramRangeID colnames(2): sample_one sample_two colData names(1): Samples > vcf_full[1:10] class: VCF dim: 10 2 genome: hg19 exptData(1): header fixed(4): REF ALT QUAL FILTER info(22): AC AF ... SB STR geno(5): AD DP GQ GT PL rownames(10): rs62224610 rs141578542 ... 22:16058463 rs149413786 rowData values names(1): paramRangeID colnames(2): sample_one sample_two colData names(1): Samples > vcf_no_info[1:10] Error in slot(x, "info")[i, , drop = FALSE] : selecting rows: subscript contains NAs or out of bounds indices > sessionInfo() R version 2.15.2 (2012-10-26) Platform: x86_64-unknown-linux-gnu (64-bit) locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=C LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C attached base packages: [1] stats graphics grDevices utils datasets methods base other attached packages: [1] VariantAnnotation_1.4.3 Rsamtools_1.10.2 Biostrings_2.26.2 [4] GenomicRanges_1.10.5 IRanges_1.16.4 BiocGenerics_0.4.0 loaded via a namespace (and not attached): [1] AnnotationDbi_1.20.2 Biobase_2.18.0 biomaRt_2.14.0 [4] bitops_1.0-5 BSgenome_1.26.1 compiler_2.15.2 [7] DBI_0.2-5 GenomicFeatures_1.10.0 parallel_2.15.2 [10] RCurl_1.95-3 RSQLite_0.11.2 rtracklayer_1.18.0 [13] stats4_2.15.2 tools_2.15.2 XML_3.95-0.1 [16] zlibbioc_1.4.0

Hi Paul, Thanks for the bug report. Now fixed in VariantAnnotation 1.5.14 in devel and 1.4.5 in release. These versions will be available Friday (11/16) 9am PST or immediately from svn. Valerie On 11/14/12 05:41, Paul Theodor Pyl wrote: > Hi all, > > I am reading in some .vcf files with the readVcf function and realized > that I cannot subset the resulting VCF objects if the info field is > empty, see example below. > > Is there a workaround except for loading the info at least partially? > > Thanks, > Paul > > The Example: > > vcf_full = readVcf("test.vcf.gz", "hg19") > > vcf_no_info = readVcf("test.vcf.gz", "hg19", param = ScanVcfParam( > geno=c("GT","GQ"), fixed="ALT", info=NA )) > vcf_full > class: VCF > dim: 71128 2 > genome: hg19 > exptData(1): header > fixed(4): REF ALT QUAL FILTER > info(22): AC AF ... SB STR > geno(5): AD DP GQ GT PL > rownames(71128): rs62224610 rs141578542 ... 22:51243743 22:51244332 > rowData values names(1): paramRangeID > colnames(2): sample_one sample_two > colData names(1): Samples > > vcf_no_info > class: VCF > dim: 71128 2 > genome: hg19 > exptData(1): header > fixed(2): REF ALT > info(0): > geno(2): GQ GT > rownames(71128): rs62224610 rs141578542 ... 22:51243743 22:51244332 > rowData values names(1): paramRangeID > colnames(2): sample_one sample_two > colData names(1): Samples > > vcf_full[1:10] > class: VCF > dim: 10 2 > genome: hg19 > exptData(1): header > fixed(4): REF ALT QUAL FILTER > info(22): AC AF ... SB STR > geno(5): AD DP GQ GT PL > rownames(10): rs62224610 rs141578542 ... 22:16058463 rs149413786 > rowData values names(1): paramRangeID > colnames(2): sample_one sample_two > colData names(1): Samples > > vcf_no_info[1:10] > Error in slot(x, "info")[i, , drop = FALSE] : > selecting rows: subscript contains NAs or out of bounds indices > > > sessionInfo() > R version 2.15.2 (2012-10-26) > Platform: x86_64-unknown-linux-gnu (64-bit) > > locale: > [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C > [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 > [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 > [7] LC_PAPER=C LC_NAME=C > [9] LC_ADDRESS=C LC_TELEPHONE=C > [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] VariantAnnotation_1.4.3 Rsamtools_1.10.2 Biostrings_2.26.2 > [4] GenomicRanges_1.10.5 IRanges_1.16.4 BiocGenerics_0.4.0 > > loaded via a namespace (and not attached): > [1] AnnotationDbi_1.20.2 Biobase_2.18.0 biomaRt_2.14.0 > [4] bitops_1.0-5 BSgenome_1.26.1 compiler_2.15.2 > [7] DBI_0.2-5 GenomicFeatures_1.10.0 parallel_2.15.2 > [10] RCurl_1.95-3 RSQLite_0.11.2 rtracklayer_1.18.0 > [13] stats4_2.15.2 tools_2.15.2 XML_3.95-0.1 > [16] zlibbioc_1.4.0 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at r-project.org > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor