Hi Shruti,

It will be fun for you to learn the NGS data analysis. For the help, you can find some interesting courses/tutorials/lessons on this link https://www.biostars.org/p/142494/.

We can be in contact if you need any assistance in understanding and learning the data analysis.

Hello Shruti,

I hope below link will help you:

http://genestack-user-tutorials.readthedocs.io/tutorials/WES_data_analysis/

and Abhijit has suggested the link you can also try that. You can ask further if you need any help.

Good luck!

A web based option if you want to get started analyzing the data without using command line tools would be to use the Galaxy server:

https://usegalaxy.org

Benjamin

Thank you so much for your suggestions. It is very helpful.

Hi Shruti Bagla Google Brain Team recently released DeepVariant which you can use as an alternative to GATK.

We implemented a reproducible version that was submitted to NF-Core (https://lifebit.page.link/UW58).

We also made it available in Lifebit (https://lifebit.page.link/os1m) if you want to try it with example parameters. There are many other analysis pipelines and feel free to request one if you do not see what you are looking for.

In practice, DeepVariant first builds images based on the BAM file, then it uses a DeepLearning image recognition approach to obtain the variants and eventually it converts the output of the prediction in the standard VCF format.