Question: Variation in coding region
gravatar for ridatariq04
2.1 years ago by
ridatariq0410 wrote:


I filtered five VCF files by using GATK tools with option "Select Variants from VCF File" and combine them by "Combine Variants". Now I am interested to check the changes in locus that caused by SNPs and InDels. Which tool I have to used for it?

I am working on rice genotyping, I manually copy and paste the positionof Chromosome in IGV to check that which SNP is present in coding and non coding region but it is tedious and time consuming. Please help me.



Rida Tariq

galaxy • 584 views
ADD COMMENTlink modified 2.1 years ago by Jennifer Hillman Jackson23k • written 2.1 years ago by ridatariq0410
gravatar for Jennifer Hillman Jackson
2.1 years ago by
United States
Jennifer Hillman Jackson23k wrote:


To simply annotate whether a SNP is in a coding or non-coding region, try the tool VCF Manipulation: VCFannotate

SnpEff is a good choice for more in depth analysis. For rice, the tool would need to be set up on a local/cloud Galaxy. More details here in a prior post: Running SnpEff on Galaxy

The tool group Phenotype Association on has other options for specific tasks. Example: aaChanges amino-acid changes caused by a set of SNPs​

Best, Jen, Galaxy team


ADD COMMENTlink written 2.1 years ago by Jennifer Hillman Jackson23k
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