Tool For Finding Indel In Which Part Of Genes

Question

[azmosavi]

Are there any tools to help us determine whether an indel lies within a specific part of the gene ( Exon, Intron, ...)?

Answer 1

[Malachi Griffith]

It sounds like you want to do indel annotation or more generally variant annotation.

Here are several existing posts related to this question.

• Predicted Impact Of Indels?
• Adding Genomic Annotations Using SnpEff and VariantAnnotator
• Snpeff - Annotating And Predicting The Effects Of Single Nucleotide Polymorphisms
• Anntools - Annotation Toolkit For Snps, Insertions/Deletions, And Copy Number Variations
• Indel Annotation Tools, Not Loss Of Function
• Anyone Know A *General* Variant (Snp/Indel) Effect Predictor / Annotator?
• What'S Are The Main Differences Between Seattleseq And Annovar?
• Variant Filtration By Exclusion Of Common Or Well-Known Variants

Answer 2

[Alex Paciorkowski]

Well sure, depends on which kind of data you are working with.

You can just look it up in UCSC browser, type in the coordinates and you can tell pretty easily.

If you have a VCF file of indels you can annotate with SeattleSeq. What kind of data do you have?