Python script to process NGS data

Question

[anasjamshed]

I want to develop a script in python that automates the conversion of FASTQ to CRAM files (BWA-MEM2, GEM, etc), to BAM files (SAMTools, etc) and to Variants (BCF Tools, etc). After that, I want to develop a web application.

Is it possible?

[Carambakaracho]

FYI, there's a dedicated workflow managers for this approach, for example snakemake, nextflow (with tower as UI), CWL.

Answer 1

[LauferVA]

.... yes it is possible; the nuances of this possibility is the subject of tens of thousands of articles, webpages, software packages, etc. I hope that helps.