README.md

Introduction

KlusterCaller-to-VCF is a shell script written to take the output from KlusterCaller software and convert it into a compressed variant calling format file (vcf.gz) using base R data manipulation functions. This VCF is compliant with formatting requirements and is readable in other programs like TASSEL.

Required Inputs

KlusterCaller-to-VCF requires three inputs:

1. A KlusterCaller formatted output - example
2. A keyfile which relates KlusterCaller output to allelic states - example
3. A string for output name (i.e., "output_example")

Both files provided to the KlusterCaller-to-VCF function must be tab delimited and marker names are case-sensitive and must match exactly.

Usage

To call on the KlusterCaller-to-VCF function, the user must call on the klustercaller_to_vcf.sh file directly using the following argument:

bash klustercaller_to_vcf.sh

This can either be in the directory where you have pulled the repository or a direct path to the location of the installation. To view the usage file for further assistance use the following command:

bash klustercaller_to_vcf.sh --help

To run the provided example and look at textual output use the following command:

bash klustercaller_to_vcf.sh \
  -k klustercaller_keyfile_example.txt \
  -c klustercaller_file_example.txt \
  -o example_output \
  -v

This will result in a compressed VCF file that looks like this example.

Package Requirements

The bash script provided in this GitHub repository requires the following to run properly:

1. R statistical coding language - link to page
2. samtools/bcftools - link to page

Please make sure you have both programs installed properly prior to running to avoid errors.