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An integrated pipeline for analysis and visualization of Population Structure and Relatedness based on genome-wide genetic variant data

R 85.04% Perl 4.95% Shell 10.01%
data-visualization population-structure relatedness plink plink2 shiny-apps genome-analysis

psrelip's Issues

Syntax error in pre_analysis_first_script.sh

Hi - I am trying to integrate your wonderful pipeline. I came across the following error when running the pre_analysis_first_script.sh script:

pre_analysis_first_script.sh: line 48: syntax error near unexpected token `elif'
're_analysis_first_script.sh: line 48: `elif [[ $VCF_FILE_NAME =~ \bcf.gz$ ]]

I added the config file path to CONF_FILE in this script.
In the psrelip.config file, I have added the path to:

  • PLINK_HOME
  • PLINK2_HOME
  • TOOL_INSTALL_DIR
  • WD
  • VCF_FILE_NAME

Can you please help me solve this error. Thanks in advance!

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