In addition to what everyone else has already said, here is a more visual workflow example (it may not be appropriate in your specific situation): From: https://software.broadinstitute.org/gatk/best-practices/bp_3step.php?case=GermShortWGS
The question is very easy. I got a FASTAQ file from Illumina technology, we have the software to analyze this file, but we want the raw data from this file. We need a kind of free soft which could let us use that information in Excel. We have experience with NGS, I just want to know if there's an easy way to convert this kind of file. Thanks!
FASTQ is your raw data... if you want to "visualize" (I think you mean you want to do something called variant calling and annotation afterwards) you need an adapter trimming first, then your reads in the FASTQ file are aligned against a reference genome (e.g. BWA) - so your input is a FASTQ file and your output file is a BAM file. The BAM file is then used by whatever software you use, to do a process called variant calling. So the output file here is a VCF file (VCF stands for Variant Call Format) - you got it now? this file is at the very end of your process... Then get yourself a variant calling tool where you can simply upload the VCF file and set the filters that you want...e.g. variant allele frequency >5%, set your frequencies for ExAC, gnomad etc.. then you end up with some variants that you can now annotate and "visualize"!
hope that helps you a little bit....actually your post is 4 years old so I hope you learned something in that time!
(Slightly redacted by WouterDeCoster to remove inappropriate language)