gbs2vcf

End-to-end GBS variant-calling for plants: QC → trimming → alignment → joint genotyping → filtered VCFs.

Usage

The repository provides convert_gbs_2_vcf.sh, a bash pipeline that runs quality assessment, demultiplexing, trimming, alignment, joint genotyping and variant filtering. Edit the REF, SAMPLE_LIST, and BARCODES variables at the top of the script to match your data, then execute:

./convert_gbs_2_vcf.sh

Example samples.txt:

sample1
sample2
sample3

Example barcodes.txt (tab-separated barcode definitions):

ACTGTA	sample1
CTTGAA	sample2
GACTAG	sample3

During demultiplexing, the pipeline calls process_radtags, which reads barcodes.txt to split raw reads by barcode into per-sample FASTQs named for the sample identifiers. Those identifiers must also appear in samples.txt, which the script uses to iterate through subsequent steps.

The final filtered VCF is written to vcf/filtered_variants.vcf.gz.