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

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


  • 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



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