Produce a single sequential FASTA sequence out of BAM I'm having problems properly looking for a solution because I'm a layman in Bioinformatics not familiar with the terminology. I'm hoping you can nudge me in the right direction, please! Thank you very much.

What I want in the end

A FASTA file containing a single sequential sequence (chromosome 1-22..) of the human genome.

What I have


23gb of "clean_data" which are .fq.gz files.
21gb of "result_alignment" which is .bam+.bai
"result_variation" indel.vcf.gz and snp.vcf.gz


What I tried

I used samtools fasta reads.bam &gt; reads.fasta which results in many lines like so:

&gt;V100005418L4C001R001322578/1
AAATAGCCCACAC...
&gt;V100005418L4C001R006084507/1
GCCATAAAGCCTA...
...


But these include many many duplicate lines and the reference genome from the human genome project GRCh38 is only 3GB in size, so I thought that this FASTA sequence needs to be properly "aligned" somehow?

Am I thinking correctly here?

I'm really confused with all of the terminology and don't know exactly what I need to look for. Could someone kindly put the process into simpler words for me?
If you just want the human chromosomes in a FASTA format, why not downloading directly the individual chromosome files (chr*.fa.gz)? 

If you don't rely on the "official" releases (for whatever reason), then what you need is first to assemble your reads into genomes, possibly (but not surely) going down to a chromosome-level resolution. Different approaches for assembly are possible/available, mainly depending on (1) what do you biologically need to answer and (2) the type of sequencing data you have - we'll need more details to be able to help you in this direction. 

The samtools fasta utility will "just" convert your reads (likely given from a sequencing facility) from an alignment (BAM) format into a reads (FASTA) format, there is no concept of chromosomes here. You won't get assembled chromosomes this way, just extract the sequence in FASTA format from your alignment file.