The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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GATK CombineGCVFs

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Quick Start

Test Data

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Test data for this app appears directly in the Discovery Environment in the Data window under Shared With Me” > luj > variant_calling.

Input File(s)

  • Use directory gatk_haplotypecaller_output from the directory above as input directory of Haplotype Caller gVCF files.
  • Use ricen_Chr12.fa as reference genome fasta file.
  • Use ricen_Chr12_target.intervals as samtools-style intervals of targets

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.

  • Default parameters only, no further configuration needed.

Advanced Use

  • You could limit the analysis to target regions in a samtools-style intervals file

Output File(s)

Expect a vcf file named gatk_combinegvcfs_output.vcf as output.

Tool Source for App

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