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Davis, Brian
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40
@davis-brian-5165
Last seen 10.5 years ago
I'm seeing an error when I read in a compress vcf, but not when I read
in the uncompressed vcf. Can anyone point me in the right direction
to figure out what I'm doing wrong? I've tried this on 3 different
vcfs with the same error (different record fails).
> # read in a complete file
> fl <- "first10K.vcf"
> vcf <- readVcf(fl, "hg19")
> vcf
class: VCF
dim: 9934 998
genome: hg19
exptData(1): header
fixed(4): REF ALT QUAL FILTER
info(39): NS DP ... HD HP
geno(6): GT VR ... GQ FT
rownames(9934): 1:69270 1:69360 ... 1:19597392 1:19597396
rowData values names(1): paramRangeID
colnames(998): A00003 A00057 ... A16457 ''
colData names(1): Samples
>
> # now try again but compress it first
> fl <- "first10K.vcf"
> compressVcf <- bgzip(fl, tempfile())
> idx <- indexTabix(compressVcf, "vcf")
> tab <- TabixFile(compressVcf, idx)
> vcf <- readVcf(tab, "hg19")
Error: scanVcf: record 4370 INFO '0/0:.:130:131:.:.' not found
path:
C:\Users\bdavis2\AppData\Local\Temp\RtmpwrXcST\file1dc84cff4177
>
> sessionInfo()
R version 2.15.1 (2012-06-22)
Platform: x86_64-pc-mingw32/x64 (64-bit)
locale:
[1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United
States.1252
[3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C
[5] LC_TIME=English_United States.1252
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] VariantAnnotation_1.2.10 Rsamtools_1.8.6
Biostrings_2.24.1 GenomicRanges_1.8.13
[5] IRanges_1.14.4 BiocGenerics_0.2.0
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.18.1 Biobase_2.16.0 biomaRt_2.12.0
bitops_1.0-4.1
[5] BSgenome_1.24.0 DBI_0.2-5 GenomicFeatures_1.8.3
grid_2.15.1
[9] lattice_0.20-10 Matrix_1.0-9 RCurl_1.95-1.1
RSQLite_0.11.2
[13] rtracklayer_1.16.3 snpStats_1.6.0 splines_2.15.1
stats4_2.15.1
[17] survival_2.36-14 tools_2.15.1 XML_3.95-0.1
zlibbioc_1.2.0
Brian
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