vcftools-stats 0.1.16

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

Quick Start

To use vcftools-stats 0.1.16, import your data in vcf format (may be gzipped)
Resources: https://vcftools.github.io/perl_module.html#vcf-stats

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