I'm working on DNA data and my task generates a pipeline VCF from Fastq file, with testing different read aliner tool and different VC tools.
Now: I want to convert FASTQ to BAM by using Bowtie2 tools. I need an example to explain that step by step in a shell command.
could you help me if you know some useful resources or open source pipelines?
The reference that I'm using isGRch37 and Data from NIST