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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BCFtools 1.8 index

Creates index for bgzip compressed VCF/BCF files for random access. CSI (coordinate-sorted index) is created by default. 

Quick Start

Test Data


Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> BCFtools_index

Input File(s)

Use SRR946914.vcf.gz from the directory above as test input.

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.

  • Use all default parameters

Output File(s)

Expect SRR946914.vcf.gz.csi as output.

Tool Source for App

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