text: user4362: 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 > reads.fasta which results in many lines like so:
  >V100005418L4C001R001322578/1
  AAATAGCCCACAC...
  >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?
  
  user4362: What I wanted to do is called "Consensus Sequence". Two steps were needed:
  $ bcftools mpileup -Ou -f ref.fa input.bam | bcftools call -Ou -mv | bcftools norm -f ref.fa Oz -o output.vcf.gz
  
  After that you can create the consensus:
  $ bcftools consensus -f ref.fa output.vcf.gz > out.fa
  
  
  user294: 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. 
  
original_text: 4362: <p>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.</p>
  
  <h1>What I want in the end</h1>
  
  <p>A FASTA file containing a single sequential sequence (chromosome 1-22..) of the human genome.</p>
  
  <h1>What I have</h1>
  
  <ul>
  <li>23gb of "clean_data" which are .fq.gz files.</li>
  <li>21gb of "result_alignment" which is .bam+.bai</li>
  <li>"result_variation" indel.vcf.gz and snp.vcf.gz</li>
  </ul>
  
  <h1>What I tried</h1>
  
  <p>I used <code>samtools fasta reads.bam &gt; reads.fasta</code> which results in many lines like so:</p>
  
  <pre><code>&gt;V100005418L4C001R001322578/1
  AAATAGCCCACAC...
  &gt;V100005418L4C001R006084507/1
  GCCATAAAGCCTA...
  ...
  </code></pre>
  
  <p>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?</p>
  
  <p>Am I thinking correctly here?</p>
  
  <p>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?</p>
   4362: <p>What I wanted to do is called "Consensus Sequence". Two steps were needed:</p>
  
  <pre><code>$ bcftools mpileup -Ou -f ref.fa input.bam | bcftools call -Ou -mv | bcftools norm -f ref.fa Oz -o output.vcf.gz
  </code></pre>
  
  <p>After that you can create the consensus:</p>
  
  <pre><code>$ bcftools consensus -f ref.fa output.vcf.gz &gt; out.fa
  </code></pre>
   294: <p>If you just want the human chromosomes in a FASTA format, why not <a href="http://hgdownload.cse.ucsc.edu/goldenpath/hg38/chromosomes/" rel="nofollow noreferrer">downloading</a> directly the individual chromosome files (<code>chr*.fa.gz</code>)? </p>
  
  <p>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. </p>
  
  <p>The <code>samtools fasta</code> <a href="http://www.htslib.org/doc/samtools.html" rel="nofollow noreferrer">utility</a> 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. </p>
  