vcftools-stats 0.1.16

By Amanda Cooksey (Unlicensed)

vcftools-stats outputs some basic statistics: the number of SNPs, indels, etc.

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 ->vcftools

Input Files

Use:

  • 20150518-173953-GVCF_Chr01.vcf.gz

 

Parameters

There are no required parameters.

 

Output Files

This analysis should generate several output files:

  • output.counts

  • output.dump

  • output.indels

  • output.legend

  • output.private

  • output.qual-tstv

  • output.samples-tstv

  • output.shared

  • output.snps

  • output.tstv

Tool Source for App

https://vcftools.github.io/perl_module.html#vcf-stats

 

 

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