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Genome STRiP Functions

Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,398Administrator, GATK Developer admin
edited September 2012 in GenomeSTRiP Documentation

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

Post edited by Geraldine_VdAuwera on

Geraldine Van der Auwera, PhD

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