I would recommend to use GSNAP for RNA-seq data. For Exome/WGS, it makes
little difference. GSNAP has recently undergone an optimization spree that
improves performance by an order of magnitude, but those changes are not
yet reflected in the version embedded within gmapR. If you do use GSNAP
with paired end data, we recommend setting clip_overlaps to TRUE, so that
overlapping ends are hard clipped and variants in the overlap are not
double counted by bam_tally.


On Mon, Nov 11, 2013 at 12:24 PM, heyi xiao <xiaoheyiyh@yahoo.com> wrote:

> Hi Steve and Martin,
> Thanks for all the suggestions. Following Martin’s suggestion, I started a
> new session using:
> R –vanilla
> Then,
> source("http://bioconductor.org/biocLite.R")
> biocLite("VariantTools")
> Now VariantTools and dependencies are installed fine.
>
> BTW, one question here: Is there any special advantage of using GSNAP
> (besides calling within R through gmapR) over BWA in reads mapping? GSNAP
> should be slower.
> Heyi
>
> --------------------------------------------
> On Mon, 11/11/13, Martin Morgan <mtmorgan@fhcrc.org> wrote:
>
>  Subject: Re: [BioC] VariantTools installation problem: dependencies not
> available
>  To: "heyi xiao" <xiaoheyiyh@yahoo.com>, "Michael Lawrence" <
> lawrence.michael@gene.com>
>  Cc: "bioconductor@r-project.org" <bioconductor@r-project.org>
>  Date: Monday, November 11, 2013, 1:32 PM
>
>  On 11/11/2013 10:10 AM, heyi xiao
>  wrote:
>  > Hi Michael,
>  > You mean that URL “
> http://bioconductor.org/packages/2.13/bioc/src/contrib/”
>  points to the old devel versions? But it looks like the 2.13
>  branch, or is it the same thing? I didn’t specify anything
>  in the installation as you see in my code, with or without
>  type="source" gives the same problem.
>  > What shall I do now? Thanks!
>
>  I can't really understand what's going wrong, but I'd start
>  by
>
>     R --vanilla
>
>  and then
>
>     source("http://bioconductor.org/biocLite.R")
>     biocLite("BiocInstaller")
>
>  which should end up with BiocInstaller v. 1.12.0
>
>     Bioconductor version 2.13 (BiocInstaller
>  1.12.0), ?biocLite for help
>
>  If there are still problems, it might be helpful to try
>  installing XVector itself
>
>     biocLite("XVector")
>
>  and visiting via a browser
>
>     http://bioconductor.org/packages/2.13/bioc/src/contrib/PACKAGES
>
>  which should have lines like
>
>     Package: XVector
>     Version: 0.2.0
>
>  to indicate that XVector_0.2.0.tar.gz should be returned. If
>  this file reports
>  something different in the web browser, e.g., Version:
>  0.1.4, then my guess is
>  that your institution has some kind of proxy mechanism in
>  place, and this is
>  stale -- you'd need to speak with your system
>  administrator.
>
>  The output of
>
>     biocinstallRepos()
>
>  might be helpful.
>
>  Martin
>
>  > Heyi
>  >
>  > --------------------------------------------
>  > On Mon, 11/11/13, Michael Lawrence <lawrence.michael@gene.com>
>  wrote:
>  >
>  >   Subject: Re: [BioC] VariantTools
>  installation problem: dependencies not available
>  >
>  >   Cc: "bioconductor@r-project.org"
>  <bioconductor@r-project.org>
>  >   Date: Monday, November 11, 2013, 12:46
>  PM
>  >
>  >   Looks like some sort of
>  >   cache or something is stale. It's
>  trying to install the
>  >   old devel versions of the Bioc 2.13
>  packages.
>  >
>  >   Michael
>  >
>  >
>  >
>  >
>  >   wrote:
>  >
>  >   I tried to install VariantTools under
>  R version 3.0.1 on my
>  >   Linux machine. It failed due to
>  dependencies not available
>  >   (error message below). Any suggestion
>  or help would be
>  >   appreciated.
>  >
>  >
>  >
>  >
>  >
>  >   > biocLite("VariantTools",
>  >   type="source")
>  >
>  >   BioC_mirror: http://bioconductor.org
>  >
>  >   Using Bioconductor version 2.13
>  (BiocInstaller 1.11.4), R
>  >   version 3.0.1.
>  >
>  >   Installing package(s) 'VariantTools'
>  >
>  >   also installing the dependencies
>  XVector, IRanges,
>  >   GenomicRanges, gmapR, BiocParallel
>  >
>  >
>  >
>  >   trying URL '
> http://bioconductor.org/packages/2.13/bioc/src/contrib/XVector_0.1.4.tar.gz
> '
>  >
>  >   Error in download.file(url, destfile,
>  method, mode =
>  >   "wb", ...) :
>  >
>  >     cannot open URL '
> http://bioconductor.org/packages/2.13/bioc/src/contrib/XVector_0.1.4.tar.gz
> '
>  >
>  >   In addition: Warning message:
>  >
>  >   In download.file(url, destfile,
>  method, mode =
>  >   "wb", ...) :
>  >
>  >     cannot open: HTTP status was
>  '404 Not Found'
>  >
>  >   Warning in download.packages(pkgs,
>  destdir = tmpd, available
>  >   = available,  :
>  >
>  >     download of package XVector
>  failed
>  >
>  >   trying URL '
> http://bioconductor.org/packages/2.13/bioc/src/contrib/IRanges_1.19.38.tar.gz
> '
>  >
>  >   Error in download.file(url, destfile,
>  method, mode =
>  >   "wb", ...) :
>  >
>  >     cannot open URL '
> http://bioconductor.org/packages/2.13/bioc/src/contrib/IRanges_1.19.38.tar.gz
> '
>  >
>  >   In addition: Warning message:
>  >
>  >   In download.file(url, destfile,
>  method, mode =
>  >   "wb", ...) :
>  >
>  >     cannot open: HTTP status was
>  '404 Not Found'
>  >
>  >   Warning in download.packages(pkgs,
>  destdir = tmpd, available
>  >   = available,  :
>  >
>  >     download of package IRanges
>  failed
>  >
>  >   …
>  >
>  >
>  >
>  >   _______________________________________________
>  >
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>  >
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>  >
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>  >
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>  > Bioconductor@r-project.org
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>  >
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>
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