tallies: Tally VRanges

In lawremi/VariantToolsData: Data for the VariantTools tutorial

Description

Nucleotide tallies computed over the TP53 region (+/- 1Mb) for the 50/50 NA12878/NA19240 mixture, separately for each replicate. Each replicate corresponds to a separate biochemical mixing.

Usage

data(tallies)

Format

A VRangesList, each VRanges of which corresponds to one of the three biochemical replicates.

Source

Computed from the alignments of the FASTQ files found in the ‘inst/extdata’ directory. Repeat regions (see repeats) were excluded. For example, for one replicate,

      library(gmapR)
      extdata.dir <- system.file("extdata",
                                 package="VariantToolsData")
      bams <- BamFileList(tools::list_files_with_exts(extdata.dir, "bam"))
      data(repeats, package = "VariantToolsData")
      param <- TallyVariantsParam(TP53Genome(), mask = repeats,
                                  read_pos=TRUE, read_length=75L)
      tallies <- split(tallyVariants(bams, param), ~ sampleNames)
  

This assumes that the BAM files have been generated for the current version of the TP53 genome:

      param <- GsnapParam(TP53Genome(), unique_only = TRUE,
                          molecule = "DNA")
      first.fastq <- dir(extdata.dir, "first.fastq",
                         full.names=TRUE)
      last.fastq <- dir(extdata.dir, "last.fastq",
                        full.names=TRUE)
      output <- gsnap(first.fastq, last.fastq, param)
      bams <- as(output, "BamFileList")
  

References

Lawrence, M., Huntley, M. A., Stawiski, E., Owen, A., Wu, T. D., Goldstein, L. D., Cao, Y., Degenhardt, J., Young, J., Guillory, J., Heldens, S., Jackson, M., Seshagiri S., and Gentleman, R. (2015). Genomic variant calling: Flexible tools and a diagnostic data set. bioRxiv.

Examples

data(tallies)
VariantTools::callVariants(tallies[[1L]])

lawremi/VariantToolsData documentation built on May 20, 2019, 8:26 p.m.