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 call

 

Quick StartTo use BCFtools 1.8 call, import your data in VCF format

Test Data

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

Input File(s)

Use mpileup_out.vcf 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 these parameters within the DE app interface:
    • Select an output file name and output file type in the output section
    • Leave all other parameters as default

Output File(s)

Expect bcftools_1.8_call_output.vcf as output.

Tool Source for App

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