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vcftools-phased-join 0.1.16

vcftools-phased-join 0.1.16

Takes multiple overlapping pre-phased chunks and concatenates them into one VCF using heterozygous calls from the overlaps to determine correct phase. 

Quick Start

  • To use vcftools-phased-join 0.1.16, import your data in vcf format (may be gzipped) along with the corresponding tbi index files

  • Resources: https://vcftools.github.io/perl_module.html#vcf-phased-join

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

  • 20150518-173953-GVCF_Chr01.vcf.gz.tbi

  • 20150518-173953-GVCF_Chr02.vcf.gz

  • 20150518-173953-GVCF_Chr02.vcf.gz.tbi

 

Parameters

There are no required parameters.

 

Output Files

This analysis should generate two output files; a phased-join VCF file made from the input files and a .plog file with summary statistics.

  • phased-join_out.vcf

  • phased-join.plog

Tool Source for App

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