This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Can I combine the GBS data with Whole Genome Resequencing for GWAS analysis

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
• 2,903 views • link
updated by behnam • behnam • written by gengyang12138 • gengyang12138

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

• 0 views • link
written by soniabedi.07 • soniabedi.07

Hi! Did you manage the issue?

• 0 views • link
written by Denis Denis

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

• 0 views • link
written by behnam • behnam

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

• 0 views • link
written by Istvan Albert Istvan Albert

Thanks. I created a new thread.

• 0 views • link
written by behnam • behnam

0 answers

No answers yet.

Log in to answer this question.

More posts like this