This page was last updated on Saturday, 13-Dec-2014 11:25:22 CST

Installation notes for gvcftools version 0.16 - Nov. 4, 2013

Home Page

Prerequisites

Installation prerequisites

Installation

1. $ ver="0.16"
2. $ cd /programinstallers/
3. $ wget https://sites.google.com/site/gvcftools/home/download/gvcftools-$ver.tar.gz -O gvcftools-$ver.tar.gz
4. $ tar -zxvf gvcftools-$ver.tar.gz
5. $ cd gvcftools-$ver
6. $ make
7. Manual installation
   $ cp -pvi bin/* /usr/local/bin/

   `bin/break_blocks' -> `/usr/local/bin/break_blocks'
   `bin/extract_variants' -> `/usr/local/bin/extract_variants'
   `bin/gatk_to_gvcf' -> `/usr/local/bin/gatk_to_gvcf'
   `bin/getBamAvgChromDepth.pl' -> `/usr/local/bin/getBamAvgChromDepth.pl'
   `bin/get_called_regions' -> `/usr/local/bin/get_called_regions'
   `bin/merge_variants' -> `/usr/local/bin/merge_variants'
   `bin/remove_region' -> `/usr/local/bin/remove_region'
   `bin/set_haploid_region' -> `/usr/local/bin/set_haploid_region'
   `bin/trio' -> `/usr/local/bin/trio'
   `bin/twins' -> `/usr/local/bin/twins'

8. Cleanup
   $ cd ..
9. $ rm gvcftools-$ver -rf