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exSTRa

expanded STR algorithm: detecting expansions with paired-end Illumina sequencing data.

This depends on the Perl package Bio::STR::exSTRa for processing of BAM files.

Installation

For easy installation, run from within R:

  # install.packages("devtools") # if devtools is not already installed
  devtools::install_github("bahlolab/exSTRa", build_vignettes = TRUE)

Using exSTRa

At present, the pipeline requires:

  • Paired-end Illumina sequencing. Has been tested with some whole-exome sequencing, and whole-genome sequencing with and without PCR in the library preparation step. (Testing on single-end data has not occured, but we presume it would perform poorly due to the affect on alignment.)
  • Alignment with bowtie2 in local mode (may work for other aligners and settings, not extensively tested due to computational time)
  • Sorting
  • PCR duplicate marking (recommended)

A database of repeats is required, with files for the known disorder loci included for hg19, GRCh37, hg38 or GRCh38 in the inst/extdata directory. A database of all STRs genome wide in available to download from FigShare. An example script to generate this database of all STRs genome wide, or those in genes that are expressed in the brain, is provide in inst/tools/prepare_exSTRa_input_db.R.

Use the Perl scripts and modules from https://github.com/bahlolab/Bio-STR-exSTRa to analyse reads in BAM files. This generates STR counts. In the future this functionality may be included within the R exSTRa package.

This R package provides an OO S3 interface. Currently makes extensive use of the data.table package, and understanding its use may help with this package.

Examples

Please see the exSTRa vignette for a workable example; this can be viewed in R after installation of the package with

vignette("exSTRa")

or can be downloaded in the repository from doc/exSTRa.html.

Other datasets in BAM/CRAM format can be analysed in a similar way after processing with the Perl Bio::STR::exSTRa package.

Help

Please visit our Discussions for help with using exSTRa. For bugs, please open a Github issue.

Citation

Rick M. Tankard, Mark F. Bennett, Peter Degorski, Martin B. Delatycki, Paul J. Lockhart, Melanie Bahlo. Detecting Expansions of Tandem Repeats in Cohorts Sequenced with Short-Read Sequencing Data. American Journal of Human Genetics, 103(6):858-873, 2018. https://doi.org/10.1016/j.ajhg.2018.10.015

Licenced under GPL-2.