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

Discovery Environment Applications List

The box below searches only this space.
To search the entire iPlant wiki, enter your query in the box at the upper right.






Skip to end of metadata
Go to start of metadata

BCFtools 1.8 view

print, extract, convert and call SNPs from BCF

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 -> Samtools_mpileup.

Input File(s)

Use input.bcf 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:
    • Check "SNP Calling" in "Consensus/variant calling option" panel
    • Check "call genotypes at variant sites" in "Consensus/variant calling option" panel
    • Check "output potential variant sites only" in "Consensus/variant calling option" panel

Output File(s)

Expect bcftools_1.8_view_output as output.

Tool Source for App

  • No labels