Which tool is best for getting genomic data analysis?

Question

[akshaykum684]

Hi,

We have VCF files which need to be analyzed. So what are some of the tools that can be used?

I have heard about

a) Bioconductor
b) Galaxy
c) BioPython
d) Hail

As I am starting with genomic data analysis, I have to pick up learning one tool. So based on your experiences, can you suggest a tool that would be good and can be used for bioinformatic data analysis?

[GenoMax]

We have VCF files which need to be analyzed.

What kind of analysis? In general bcftools already mentioned below is a tool box for manipulation of VCF files.

Answer 1

[Pierre Lindenbaum]

a , b and c are not 'tools'.

So based on your experiences, can you suggest a tool that would be good and can be used for bioinformatic data analysis?

bcftools.

[akshaykum684]

Hi, Thanks for the response. I see that Galaxy is a viewer. But May I know why Bioconductor and BioPython packages cannot be used for analysis? I was seeing some courses in Coursera which teach courses for genomic data analysis based on these tools.

Can I kindly request you to help me understand the difference please?

In addition, Isn't hail widely used? When do we use Hail?

[Pierre Lindenbaum]

bioconductor is a set of many R packages, biopython is an API.

[h.mon]

Galaxy is not a "viewer". Shortly, Galaxy is both a web interface (frontend), with an graphical interface to several bioinformatics software (backend). This, Galaxy allows researchers without informatics experience to perform complex analyses. Read more at Galaxy 101 - What is Galaxy?

[Devon Ryan]

Hail is primarily used by those doing GWAS, otherwise I've never seen it used.

[Ram]

In my previous team, we used hail as a stand-in for plink. It gave us a way to look at IBD/IBS and relatedness among individuals in gigantic VCF files - I'm not sure if that counts as GWAS.