BCFTOOLS-1.13 VCF-Utilities varFilter

filters short variants in a VCF file

Quick Start

To use BCFTOOLS-1.13 VCF-Utilities varFilter, import your data in vcf format.

Resources: https://github.com/samtools/bcftools/blob/develop/misc/vcfutils.pl

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 bcftools_view_output 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.

Default parameters only, no further configuration needed.

Output File(s)

Expect vcfutils_varFilter_output as output.

Tool Source for App

https://github.com/samtools/bcftools/blob/develop/misc/vcfutils.pl

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