Answers.Body: <h3>NA12878</h3>
  
  <ul>
  <li><p>My recommendation: download raw reads from <a href="https://basespace.illumina.com/home/index" rel="nofollow noreferrer">Illumina BaseSpace</a> and do alignment yourself. Aligning ~40X worth of human reads takes overnight with ~16 CPU cores.</p></li>
  <li><p>You can acquire <a href="https://www.illumina.com/platinumgenomes.html" rel="nofollow noreferrer">Platinum Genome</a> data <a href="https://www.ebi.ac.uk/ena/data/view/ERX168836" rel="nofollow noreferrer">from ENA</a>. There is a BAM available for download, but that was done by Illumina's own aligner against a wrong reference genome. You'd better do alignment by yourself. Another problem with this dataset is it is too good to be representative. Modern data are worse.</p></li>
  <li><p>GIAB provides BAMs here:</p>
  
  <pre><code>ftp://ftp-trace.ncbi.nih.gov/giab/ftp/data/NA12878/NIST_NA12878_HG001_HiSeq_300x/
  </code></pre>
  
  <p>It is not "typical", either.</p></li>
  </ul>
  
  <h3>SGDP</h3>
  
  <ul>
  <li><p>Instructions on downloading SGDP BAMs are available <a href="https://www.simonsfoundation.org/simons-genome-diversity-project/" rel="nofollow noreferrer">on this page</a>, in particular <a href="http://simonsfoundation.s3.amazonaws.com/share/SCDA/datasets/2014_11_12/StepstodownloadtheSGDPdataset_v4.docx" rel="nofollow noreferrer">this Word document</a>. Warning: you need ~30TB disk space for these BAMs. I also heard it is tricky to download data.</p></li>
  <li><p>There is apparently a mirror <a href="https://docs.cancergenomicscloud.org/v1.0/docs/simons-genome-diversity-project-sgdp-dataset" rel="nofollow noreferrer">from cancer genomics cloud</a>. I don't know how easy it is to access.</p></li>
  </ul>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-25T17:40:24.347Z
Answers.Text: I'm having some trouble finding the fastq files for NA12878 on Illumina BaseSpace. Do you have any suggestions on where to find these?
Answers.UserDisplayName: Jon Deaton
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2018-06-23T01:43:49.577Z
Answers.LastActivityDate: 2018-06-23T01:43:49.577Z
Answers.UserDisplayName: user172818
Body: <p>I am doing a project that requires bench-marking the performance of computational tools for alignment and variant calling of human genome sequencing data. In particular I would like to establish benchmarks comparing the performance of <a href="https://software.broadinstitute.org/gatk/" rel="nofollow noreferrer">GATK</a> and <a href="https://github.com/bigdatagenomics/adam" rel="nofollow noreferrer">ADAM</a>/<a href="https://github.com/bigdatagenomics/avocado" rel="nofollow noreferrer">Avocado</a>. </p>
  
  <p>My main question is which genomic data-sets should I use as the input to the data processing pipeline. In Frank Nothaft's (author of ADAM and Avodaco) <a href="https://www2.eecs.berkeley.edu/Pubs/TechRpts/2017/EECS-2017-204.html" rel="nofollow noreferrer">thesis</a> he reports bench-marking the processing of NA12878 from the 1,000 genome's project in Avocado as compared to GATK's HalotypeCaller. He also reports benchmarking on 270 samples from the Simons Genome Diversity Data-set.</p>
  
  <p>I am interested in reproducing this portion of his work, but do not know where I can get a hold of these datasets. Where can I get a copy of the NA12878 genome (BAM file) and also were can I get aligned samples from Simons Genome Diversity Data-set? </p>
  
Tags: <gatk><adam>
Title: Human Genome Alignment and Variant Calling Benchmarks
ThreadText: # Human Genome Alignment and Variant Calling Benchmarks
  
  (Asked by: username_0 on 2018-06-22)
  
  I am doing a project that requires bench-marking the performance of computational tools for alignment and variant calling of human genome sequencing data. In particular I would like to establish benchmarks comparing the performance of [GATK](https://software.broadinstitute.org/gatk/) and [ADAM](https://github.com/bigdatagenomics/adam)/[Avocado](https://github.com/bigdatagenomics/avocado).
  
  My main question is which genomic data-sets should I use as the input to the data processing pipeline. In Frank Nothaft's (author of ADAM and Avodaco) [thesis](https://www2.eecs.berkeley.edu/Pubs/TechRpts/2017/EECS-2017-204.html) he reports bench-marking the processing of NA12878 from the 1,000 genome's project in Avocado as compared to GATK's HalotypeCaller. He also reports benchmarking on 270 samples from the Simons Genome Diversity Data-set.
  
  I am interested in reproducing this portion of his work, but do not know where I can get a hold of these datasets. Where can I get a copy of the NA12878 genome (BAM file) and also were can I get aligned samples from Simons Genome Diversity Data-set?
  
  **Tags:** gatk, adam
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2018-06-23. Score: 2 | Accepted answer
  
  ### NA12878
  
  * My recommendation: download raw reads from [Illumina BaseSpace](https://basespace.illumina.com/home/index) and do alignment yourself. Aligning ~40X worth of human reads takes overnight with ~16 CPU cores.
  * You can acquire [Platinum Genome](https://www.illumina.com/platinumgenomes.html) data [from ENA](https://www.ebi.ac.uk/ena/data/view/ERX168836). There is a BAM available for download, but that was done by Illumina's own aligner against a wrong reference genome. You'd better do alignment by yourself. Another problem with this dataset is it is too good to be representative. Modern data are worse.
  * GIAB provides BAMs here:
  
    ```
    ftp://ftp-trace.ncbi.nih.gov/giab/ftp/data/NA12878/NIST_NA12878_HG001_HiSeq_300x/
  
    ```
  
    It is not "typical", either.
  
  ### SGDP
  
  * Instructions on downloading SGDP BAMs are available [on this page](https://www.simonsfoundation.org/simons-genome-diversity-project/), in particular [this Word document](http://simonsfoundation.s3.amazonaws.com/share/SCDA/datasets/2014_11_12/StepstodownloadtheSGDPdataset_v4.docx). Warning: you need ~30TB disk space for these BAMs. I also heard it is tricky to download data.
  * There is apparently a mirror [from cancer genomics cloud](https://docs.cancergenomicscloud.org/v1.0/docs/simons-genome-diversity-project-sgdp-dataset). I don't know how easy it is to access.
  
  > **Comments:**
  > **username_0**: I'm having some trouble finding the fastq files for NA12878 on Illumina BaseSpace. Do you have any suggestions on where to find these?  
  
  ---
  
  