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 merge VCF

Merge multiple VCF/BCF files from non-overlapping sample sets to create one multi-sample file.

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_merge

Input File(s)

Use the following files from the directory above as test input.

Input VCF/BCF files:
  • SRR946914.vcf.gz
  • SRR946916.vcf.gz
Index files:
  • SRR946914.vcf.gz.csi 
  • SRR946916.vcf.gz.csi 

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.S

  • Set the output file name to '14_16_merged.vcf'
  • Choose 'uncompressed VCF' as the output file type
  • All other parameters may be left as default.

Output File(s)

Expect 14_16_merged.vcf as output.

Tool Source for App

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