Can I combine the GBS data with Whole Genome Resequencing for GWAS analysis

Question

[gengyang12138]

My boss give me some GBS (Genotyping-by-Sequencing) data, want me to make GWAS analysis with the Whole Genome Resequencing data download from NCBI. I don't know can I combine two different type data to analysis.

In my preanalysis, I used GATK pipeline to call SNP from GBS and Whole Genome Resequencing data. But I found the number of SNP in Whole Genome Resequencing data is far greater than GBS. In GBS data, I just got hundreds of thousands of SNP, howevent, the number in Whole Genome Resequencing data is Tens of millions.

So, I want to know, is the wide difference of SNP due to different data type, and can I make analysis combine these data. If I can, which software should I do.

[soniabedi.07]

GBS is usually low coverage sequencing, the reads are limited as compared to whole genome sequencing. This difference shows in SNPs detected.

[Denis]

Hi! Did you manage the issue?

[behnam]

I have the same issue in Brassica Juncea. Can we combine GBS and WGS data for variant caling in GWAS? Is there any recommendation?

[Istvan Albert]

please ask the question as a separate post not as a comment in a 6 year old thread

[behnam]

Thanks. I created a new thread.