Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-01-22T18:31:42.317Z
Answers.LastActivityDate: 2020-01-22T18:31:42.317Z
Answers.UserDisplayName: Daniel Biegler
Answers.Body: <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>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-07-05T13:57:17.370Z
Answers.Text: Thank you very much for your input! I don't have something biologically to answer, this project revolves about sequencing(?) this specific individuals DNA. I need the DNA from "start to finish" so to speak, Chr1 to Chr22, X,Y in ascending order, is what I'm trying to say. I understand now that the FASTA conversion is not what I need, I need to assemble my reads first. As for data I have: 23gb of "clean_data" which are .fq.gz files. 21gb of "result_alignment" which is .bam+.bai and I got "result_variation" indel.vcf.gz and snp.vcf.gz. Can I use these to achieve what I want? Thank you very much!
Answers.UserDisplayName: Daniel Biegler
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Answers.CreationDate: 2019-07-05T15:43:33.823Z
Answers.Text: Usually when you sequence a person's genome, you're trying to identify variants that the individual has, compared to the reference genome. In that case, you should do what @aechchiki said, and download the official reference FASTAs, and create a VCF file containing all the variants for that individual.
  
  Alternatively, it also sounds like you might be trying to do _de novo_ genome assembly. That is a very different topic from variant calling, and that would give you a "reference" that is very different from the reference genome builds mentioned above
Answers.UserDisplayName: James Hawley
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Answers.CreationDate: 2019-07-05T17:10:48.230Z
Answers.Text: @DanielBiegler please [edit] your question and tell us _why_ you are sequencing this individual since the data you will require will depend on what you are trying to do. It is extremely unlikely that you need the individual's full genome rather than the specific locations where their genome differs from the reference (variants). But if you don't us what biological question you are trying to answer using the individual's sequence, then we can't really help much.
Answers.UserDisplayName: terdon
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Answers.LastEditDate: 2019-07-05T07:50:05.420Z
Answers.UserDisplayName: aechchiki
Body: <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>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-07-05T05:21:21.160Z
Comments.Text: What you have in BAM format is an alignment of reads to a reference. What you are looking for (a single fasta per chromosome) is a new assembly. Using "samtools fasta" will just get you each read in fasta format, which is clearly not what you want. In addition to doing a (de novo) assembly of your reads you could make a (reference-guided) consensus sequence. You can find some pointers on how to do that here: https://www.biostars.org/p/367960/
Comments.UserDisplayName: Wouter De Coster
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-07-05T14:05:26.490Z
Comments.Text: Thank you so much for your comment @Wouter. The link you posted sounds very promising. I will try it out and get back to you. Meanwhile I clarified in my post what kind of data I have. Maybe you want to take a deeper look. Thanks again!
Comments.UserDisplayName: Daniel Biegler
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-07-05T14:23:38.553Z
Comments.Text: another option is to take the reference genome you used for alignment, and 'mutate' it with the variants you identified. One tool to do that is GATK FastaAlternateReferenceMaker. I don't know how well it deals with indels though.
  And keep in mind that the sample which you sequenced is diploid. If you want one fasta sequence per chromosome for that individual then you have to think about how to handle heterozygous sites. If you want one paternal and one maternal fasta then you are in bigger trouble because you need to know on which phase the variants are relative to each other.
Comments.UserDisplayName: Wouter De Coster
Tags: <sam><phylogenetics><ngs><genome-sequencing>
Title: Produce a single sequential FASTA sequence out of BAM
ThreadText: # Produce a single sequential FASTA sequence out of BAM
  
  (Asked by: username_0 on 2019-07-04)
  
  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?
  
  **Tags:** sam, phylogenetics, ngs, genome-sequencing
  
  > **Comments:**
  > **username_1**: What you have in BAM format is an alignment of reads to a reference. What you are looking for (a single fasta per chromosome) is a new assembly. Using "samtools fasta" will just get you each read in fasta format, which is clearly not what you want. In addition to doing a (de novo) assembly of your reads you could make a (reference-guided) consensus sequence. You can find some pointers on how to do that here: https://www.biostars.org/p/367960/  
  > **username_0**: Thank you so much for your comment @username_1. The link you posted sounds very promising. I will try it out and get back to you. Meanwhile I clarified in my post what kind of data I have. Maybe you want to take a deeper look. Thanks again!  
  > **username_1**: another option is to take the reference genome you used for alignment, and 'mutate' it with the variants you identified. One tool to do that is GATK FastaAlternateReferenceMaker. I don't know how well it deals with indels though. And keep in mind that the sample which you sequenced is diploid. If you want one fasta sequence per chromosome for that individual then you have to think about how to handle heterozygous sites. If you want one paternal and one maternal fasta then you are in bigger trouble because you need to know on which phase the variants are relative to each other.  
  
  ---
  
  ## 2 answers
  
  ### Answer by username_0 on 2020-01-22. Score: 2 | Accepted answer
  
  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
  
  ```
  
  
  ---
  
  ### Answer by username_2 on 2019-07-05. Score: 3
  
  If you just want the human chromosomes in a FASTA format, why not [downloading](http://hgdownload.cse.ucsc.edu/goldenpath/hg38/chromosomes/) 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](http://www.htslib.org/doc/samtools.html) 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.
  
  > **Comments:**
  > **username_0**: Thank you very much for your input! I don't have something biologically to answer, this project revolves about sequencing(?) this specific individuals DNA. I need the DNA from "start to finish" so to speak, Chr1 to Chr22, X,Y in ascending order, is what I'm trying to say. I understand now that the FASTA conversion is not what I need, I need to assemble my reads first. As for data I have: 23gb of "clean_data" which are .fq.gz files. 21gb of "result_alignment" which is .bam+.bai and I got "result_variation" indel.vcf.gz and snp.vcf.gz. Can I use these to achieve what I want? Thank you very much!  
  > **username_3**: Usually when you sequence a person's genome, you're trying to identify variants that the individual has, compared to the reference genome. In that case, you should do what @username_2 said, and download the official reference FASTAs, and create a VCF file containing all the variants for that individual.  Alternatively, it also sounds like you might be trying to do _de novo_ genome assembly. That is a very different topic from variant calling, and that would give you a "reference" that is very different from the reference genome builds mentioned above  
  > **username_4**: @username_0 please [edit] your question and tell us _why_ you are sequencing this individual since the data you will require will depend on what you are trying to do. It is extremely unlikely that you need the individual's full genome rather than the specific locations where their genome differs from the reference (variants). But if you don't us what biological question you are trying to answer using the individual's sequence, then we can't really help much.  
  
  ---
  
  