Answers.Body: <p>You can download HGDP data in FASTQ format here: <a href="https://www.internationalgenome.org/data-portal/data-collection/hgdp" rel="nofollow noreferrer">https://www.internationalgenome.org/data-portal/data-collection/hgdp</a></p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2020-07-27T10:03:45.767Z
Answers.LastActivityDate: 2020-07-27T10:03:45.767Z
Answers.UserDisplayName: Dan Bolser
Body: <p>I need to obtain sample data from modern humans in fasta format. I just need some megabytes of data from every individual. I actually use a script that obtains the cram file from here (ftp.1000genomes.ebi.ac.uk) and then processes it to obtain the fasta file. 
  <strong>The problem is that cram files are large, slow to download and slow to process. It takes days to get the samples.
  Is there a better way to get these samples in fasta format?</strong></p>
  
  <p>The script already makes use of samtools to retrieve only the part of the bam file it needs but doesn't help much. Cram files are still gigabytes large for only a few megabytes of data that I need.</p>
  
  <p>I have the same problem with data from the 1000 genomes project.</p>
  
Comments.ContentLicense: CC BY-SA 4.0
Comments.CreationDate: 2019-12-23T20:01:14.517Z
Comments.Text: Could you please [edit] your question and clarify a bit? You say "*I just need some megabytes of data from every individual*", what individuals? Everyone in the 1000 genomes project? Then, you say "*I have the same problem with data from the 1000 genomes project.*, what other data are you looking at? Also, what do you _really_ need? Does it _have_ to be from the 1000 genomes project? Do you just need X megabases of sequence from Y individuals and don't care where it comes from? Finally, do you want fasta or fastq?
Comments.UserDisplayName: terdon
Tags: <fasta><samtools><human-genome><1000genomes>
Title: Obtaining HGDP project data in fasta format
ThreadText: # Obtaining HGDP project data in fasta format
  
  (Asked by: username_0 on 2019-12-20)
  
  I need to obtain sample data from modern humans in fasta format. I just need some megabytes of data from every individual. I actually use a script that obtains the cram file from here (ftp.1000genomes.ebi.ac.uk) and then processes it to obtain the fasta file.
  **The problem is that cram files are large, slow to download and slow to process. It takes days to get the samples.
  Is there a better way to get these samples in fasta format?**
  
  The script already makes use of samtools to retrieve only the part of the bam file it needs but doesn't help much. Cram files are still gigabytes large for only a few megabytes of data that I need.
  
  I have the same problem with data from the 1000 genomes project.
  
  **Tags:** fasta, samtools, human-genome, 1000genomes
  
  > **Comments:**
  > **username_1**: Could you please [edit] your question and clarify a bit? You say "*I just need some megabytes of data from every individual*", what individuals? Everyone in the 1000 genomes project? Then, you say "*I have the same problem with data from the 1000 genomes project.*, what other data are you looking at? Also, what do you _really_ need? Does it _have_ to be from the 1000 genomes project? Do you just need X megabases of sequence from Y individuals and don't care where it comes from? Finally, do you want fasta or fastq?  
  
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  ## 1 answers
  
  ### Answer by username_2 on 2020-07-27. Score: 0 | Accepted answer
  
  You can download HGDP data in FASTQ format here: <https://www.internationalgenome.org/data-portal/data-collection/hgdp>
  
  
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