Hi ,
I am working on the vcf files from GATK pipeline(usually around
400Mb/file), but I encountered some problems importing vcf files in R
using VariantAnnotation package, this has been confirmed in both released
and devel version of VariantAnnotation, I only provide sessionInfo for
devel-branch. I may not have the permission to provide the data here, I
just post here first to see if there is an obvious answer I don't know yet,
if any data and reproducible example are needed, I could work on that.
I don't know it's an issue in R, samtools or GATK... and I have no problem
importing vcf files from just bcftools pipeline.
If you need any details like command pipeline and version of other
software, please let me know. Thanks a lot.
Tengfei
> scanVcfHeader("~/GATK-64/GATK_AUTOMATION/VCF/Adams.vcf")
Adams.vcf
> hdr = scanVcfHeader("~//GATK-64/GATK_AUTOMATION/VCF/Adams.vcf")
*** caught segfault ***
address (nil), cause 'memory not mapped'
Traceback:
1: .Call(.scan_bcf_header, .extptr(file))
2: scanBcfHeader(bf)
3: scanBcfHeader(bf)
4: (function (file, mode) { bf <- open(BcfFile(file, character(0),
...)) on.exit(close(bf)) scanBcfHeader(bf)})(dots[[1L]][[1L]])
5: mapply(FUN = f, ..., SIMPLIFY = FALSE)
6: .Method(..., f = f)
7: eval(expr, envir, enclos)
8: eval(.dotsCall, env)
9: eval(.dotsCall, env)
10: standardGeneric("Map")
11: Map(function(file, mode) { bf <- open(BcfFile(file, character(0),
...)) on.exit(close(bf)) scanBcfHeader(bf)}, file, ...)
12: scanBcfHeader(file, ...)
13: scanBcfHeader(file, ...)
14: scanVcfHeader("~/GATK-64/GATK_AUTOMATION/VCF/Adams.vcf")
15: scanVcfHeader("~/GATK-64/GATK_AUTOMATION/VCF/Adams.vcf")
My sessioninfo
R Under development (unstable) (2013-02-17 r61981)
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] parallel stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] VariantAnnotation_1.5.38 Rsamtools_1.11.16 Biostrings_2.27.11
[4] GenomicRanges_1.11.29 IRanges_1.17.32 BiocGenerics_0.5.6
loaded via a namespace (and not attached):
[1] AnnotationDbi_1.21.10 Biobase_2.19.2 biomaRt_2.15.0
[4] bitops_1.0-5 BSgenome_1.27.1 DBI_0.2-5
[7] GenomicFeatures_1.11.11 RCurl_1.95-3 RSQLite_0.11.2
[10] rtracklayer_1.19.9 stats4_3.0.0 tools_3.0.0
[13] XML_3.95-0.1 zlibbioc_1.5.0
--
Tengfei Yin
MCDB PhD student
1620 Howe Hall, 2274,
Iowa State University
Ames, IA,50011-2274
[[alternative HTML version deleted]]
_______________________________________________
Bioc-devel@r-project.org mailing list
https://stat.ethz.ch/mailman/listinfo/bioc-devel
