Developing my own NGS pipeline

Question

[ManuelDB]

I am a trainee bioinformatician working in a genomics lab. For learning proposes I want to develop my own NGS pipeline (from fastq file to VCF file).

it would be great if someone could please pass me links where I can step by step understand the different process. It is difficult to find resources that explain in detail data needed, program available and so on.

Thanks!

EDIT: I could take the pipeline of my lab but this makes things very easy and I wouldnt learnt as much as if I create from scratch

Answer 1

[GenoMax]

See this pipeline used for analysis of cancer samples at GDC/NCI.