Question: Can I combine the GBS data with Whole Genome Resequencing for GWAS analysis
gravatar for gengyang12138
10 months ago by
China/Sichuan/Sichuan University
gengyang121380 wrote:

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.

sequencing snp • 423 views
ADD COMMENTlink written 10 months ago by gengyang121380

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

ADD REPLYlink written 5 months ago by soniabedi.0710
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