Visualize and access gvcf/vcf files

Question

[QX]

Hi all,

I had performed analysis of WGS on a iPSC cell-line and finding indels/SNPs for these cells. Now I want to explore and visualize these gvcf/vcf file for laypersons. Given no genes/disease of interest, is there any current available tool or any approach for exploring files or to track/access a SNP/gene location?.

[vinayjrao]

Hi,

You could easily load the vcf file and the reference genome on any genome browser (eg; igv tools) and view them. I don't understand the purpose of just visualizing them without having a target gene of interest, but to answer your question. This is one way.

You could go through these resources to understand how to upload and view them

https://bioinformatics-core-shared-training.github.io/intro-to-IGV/InspectingVariantsInIGV.html

https://igv.org/workshops/March2017/SlidesHandouts/IGV_Exercise_4_VariantsVCF.pdf

Hope this helps