interpreting SnpEff output
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23 months ago
Alireza ▴ 30

Hi all.

I ran GATK germline variant discovery on my WES samples.

By running SnpEff on VCF files, many intron variants have been reported.

enter image description here

Why?

Because my sequences are related to exon regions, I expected to see no intron variants in the SnpEFF output.

NGS SnpEff annotating WGS WES • 637 views
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Entering edit mode
23 months ago
Prash ▴ 280

It could be because of capture method If it were Agilent sureselect Chemistry, V8 + NCV or 5' UTR. Or even the previous versions entails subtle noncoding regions

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