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

Answer 1

[venkat]

Hello,

You can also check out SCI-VCF. As it comes with a GUI, VCF files can easily be analysed, summarised, compared, inspected and visualized without any programming. All the visualizations are also interactive and exploratory analysis can be conducted. If the VCF file sizes are small, the tool can be used installation-free through the online version.

The below resources can be helpful for a quickstart:

SCI-VCF

Documentation

Github