Genome STRiP Functions

Geraldine_VdAuwera

1. Introduction

The building blocks for Genome STRiP are built out of GATK Walkers and some miscellaneous command line utilities.

If you need to implement a specialized pipeline, you can use these modules directly, using the standard Queue pipelines as a guide. The standard Queue pipelines also use Samtools, BWA and some Picard utilities.

2. GATK Walkers

ComputeInsertSizeDistributions

ComputeReadDepthCoverage

ComputeReadSpanCoverage

SVAltAlignerWalker

SVDiscoveryWalker

SVGenotyperWalker

3. Utilities

ComputeGenomeMask

ComputeGenomeMaskStatistics

ComputeInsertStatistics

GenerateAltAlleleFasta

MergeDiscoveryOutput

MergeGenotyperOutput

MergeInsertSizeDistributions

MergeReadDepthCoverage

MergeReadSpanCoverage

4. Pre-Release

This section documents various utilities and walkers that are not yet available in the production release. These utilities may be available in some of the interim releases (build snapshots) downloadable from our website http://www.broadinstitute.org/software/genomestrip.

PlotGenotypingResults

PlotInsertSizeDistributions

mike_boursnell

Hi. Where can I take a look at the Standard Queue pipelines for SV discovery? Preferably in a form I can undertsnad without knowing about scala?

bhandsaker

Learning scala may be unavoidable :).

If you have downloaded Genome STRiP, you can look at SVDiscovery.q (which must be run after SVPreprocess.q). These "outer" scripts are designed to be relatively simple to make the steps and dependencies easier to understand. Another good tool is to run the scripts omitting the "-run" option which will cause Queue to perform a dry run (like "make -n"). There is also a presentation from a recent workshop that may be helpful: http://www.broadinstitute.org/files/shared/mpg/nextgen2011/nextgen2011_handsaker.pdf