Combine GBS and WGS data for variant calling in GWAS analysis

Question

[behnam]

We have Genotyping-by-Sequencing (GBS) data for 117 Brassica Juncea population and Whole-Genome-Sequence (WGS) data for the two parental genotypes.

Since the sequencing platforms are different, I am not sure we can combine the GBS and WGS data in the same study for variant calling and GWAS analyis.

Any comment is appreciated.

Behnam

[Denis]

Which sequencing platforms were used in both cases?

Answer 1

[Istvan Albert]

It all depends what the goals are.

You should be able to combine data for the regions covered for both platforms and produce valid results for those regions.

The problem is mostly reconciling the missing variants due to the lack of data.

[behnam]

Thanks for your comment.

I think in your comment, you mean we should analyze the parents and population separately, then combine the covered regions by both.

The data are already analyzed separately (parents and population separately) using GATK pipeine for variant calling and GAPIT for GWAS analysis.

However, I could not find any publication using this method in GWAS.

The final goal is detecting candidate genes for anthocyanin biosynthesis.