Hi,

I have question regarding accessing particular ranges of a VCF file that
I've loaded into R.

The VCF file that I've load is relatively small (~8MB). And I would like to
take subsets of the vcf file that falls into a particular genomic range.
Reading the tutorial shows that how I may use the "params" parameter in the
readVcf() function for this. But this requires me to generate a tabix file
for the vcf. I was under the impression that this is useful for big vcf
situations.

But given the fact that I've been able to load the entire VCF file into
memory already, I don't see an easy way to just generate a subset of the
vcf file given a set of genomic ranges. Is there no way to do this without
having to first generate a tabix file?

Thanks,

R version 3.0.2 (2013-09-25)
Platform: x86_64-unknown-linux-gnu (64-bit)

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C
LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8
LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=en_US.UTF-8
      LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C
            LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  grid      stats     graphics  grDevices utils     datasets
 methods   base

other attached packages:
 [1] VariantAnnotation_1.8.10 Rsamtools_1.14.2         Biostrings_2.30.1
     GenomicRanges_1.14.4     XVector_0.2.0            IRanges_1.20.6
    BiocGenerics_0.8.0       reshape2_1.2.2           ggplot2_0.9.3.1
   dplyr_0.1                mclust_4.2               stringr_0.6.2
   plyr_1.8                 xtable_1.7-1
[15] fields_6.9.1             maps_2.3-6               spam_0.40-0
     knitr_1.5                argparse_0.5.3           proto_0.3-10
    vimcom.plus_0.9-92       setwidth_1.0-3           colorout_0.9-9

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.24.0   assertthat_0.1         Biobase_2.22.0
biomaRt_2.18.0         bitops_1.0-6           BSgenome_1.30.0
 colorspace_1.2-4       DBI_0.2-7              dichromat_2.0-0
 digest_0.6.4           evaluate_0.5.1         formatR_0.10
GenomicFeatures_1.14.2 getopt_1.20.0          gtable_0.1.2
[16] labeling_0.2           MASS_7.3-29            munsell_0.4.2
 RColorBrewer_1.0-5     Rcpp_0.10.6            RCurl_1.95-4.1
rjson_0.2.13           RSQLite_0.11.4         rtracklayer_1.22.3
scales_0.2.3           stats4_3.0.2           tools_3.0.2
 XML_3.98-1.1           zlibbioc_1.8.0

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