Question

Variants in Exon or Intron

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6.0 years ago

zakkaknadine ▴ 10

After getting the variants using gatk pipeline, how can I know if the variant is in an exon or intron?

exon intron variant • 1.4k views

ADD COMMENT • link updated 6.0 years ago by shawn.w.foley ★ 1.3k • written 6.0 years ago by zakkaknadine ▴ 10

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search this site for 'functional annotation vcf'

ADD REPLY • link 6.0 years ago by Pierre Lindenbaum 166k

score 0 · Answer 1 · 2019-05-09

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6.0 years ago

shawn.w.foley ★ 1.3k

Look into snpEff, it'll classify SNPs based on location, effect on the protein (if they're in exons) and the potential for them to be low, medium, or highly disruptive.

ADD COMMENT • link 6.0 years ago by shawn.w.foley ★ 1.3k