GATK CombineGCVFs

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Quick Start

• To use GATK CombineGCVFs, import your GATK HaplotypeCaller output data in vcf format and reference genome in fasta format.
• *Resources: https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_variantutils_CombineGVCFs.php

Test Data

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

• https://www.broadinstitute.org/gatk/guide/tooldocs/org_broadinstitute_gatk_tools_walkers_variantutils_CombineGVCFs.php