This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Human Exome Variant Reference

Hi,

I want to compare the variants for my WES analysis result using Illumina/hap.py. However I cant find the reference variants for the whole exome. I know that files (vcf, bed) in GiaB are usually used as reference variants, but I don't know which file can be used as reference variants for WES. I only could find the WGS variant references in GiaB...

I know that I can use the same reference vcf as WGS, but only change the bed file to high-confident WES parts. Where could I find the bed file for WES in GiaB?

I would appreciate it if someone let me know if the analysis method I know is wrong.

Thanks.

variant-calling next-gen giab
• 1,669 views • link
updated by Jeremy Leipzig Jeremy Leipzig • written by qhtjrmin • qhtjrmin

3 answers

I think you can go ahead and take up high confidence WGS variants itself as they will contain high confidence exonic variants as well. Of course, you may need to filter off non-exonic variants, as you mentioned.

• 0 views • link
written by prasundutta87 prasundutta87

Thanks for the reply, I created and used a new bed file with the intersection of exonic parts bed and high-confident WGS variants bed. However, despite using the same variant calling tool (of course, I used the version for WES), the precision, recall, and F1-score dropped significantly compared to WGS. I think there is a problem with my comparison method because the tools I used are already proven tools. Is there anyone who has an idea about this point?

• 0 views • link
written by qhtjrmin • qhtjrmin

We offer the high-confidence regions as an option in our variant benchmarking workflow: https://truwl.com/workflows/library/Variant%20Benchmarking/0.2

highconf

• 0 views • link
written by Jeremy Leipzig Jeremy Leipzig

Log in to answer this question.

More posts like this