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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Calling SNPs INDELs with SAMtools BCFtools


Calling SNPs INDELs with SAMtools BCFtools employs SAMtools 1.7 mpileup and BCFtools 1.8 call to call SNPs and INDELs

Quick Start

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 ex1.bam from the directory above as bam input and ex1.fa from the directory above as reference sequence.

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:
    • Set the mpileup output filename. 
    • Set the BCFtools call output filename and set the output file type to uncompressed VCF.
    • Leave all other parameters as default.

Output File(s)

The output file in the example data generated with these settings is  bcftools_1.8_call_output.vcf as output.

Tool Source for App

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