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

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5.4 years ago

gengyang12138 ▴ 20

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 • 1.4k views

ADD COMMENT • link 5.4 years ago by gengyang12138 ▴ 20

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