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Variant calling in WES vs WGS

I used SnpEff tool to annotate variants in whole exome sequencing data. However, most variants in the results came out as intron and intergenic variant types. What can be the reason behind it?

I couldn't find a specific command for WES data in the snpEff documentation, so I ran the default command using the latest gene annotation file for my species.

snpeff wgs snps wes
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updated by Prash • Prash • written by fifty_fifty • fifty_fifty

2 answers

today I learned there were non-human exome kits

i guess model organisms would be very conserved in gene coding regions?

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written by Jeremy Leipzig Jeremy Leipzig

It all depends on the capture as well. It could be because of Agilent Sureselect V8 + NCV

Even otherwise, that is a good news as genetic variation is best seen in NC regions

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written by Prash • Prash

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