<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>

CC BY-SA 4.0
2018-06-25T17:40:24.347Z
I'm having some trouble finding the fastq files for NA12878 on Illumina BaseSpace. Do you have any suggestions on where to find these?
Jon Deaton
CC BY-SA 4.0
2018-06-23T01:43:49.577Z
2018-06-23T01:43:49.577Z
user172818
<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>

<gatk><adam>
Human Genome Alignment and Variant Calling Benchmarks
# 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

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## 1 answers

### Answer by username_1 on 2018-06-23. Score: 2 | Accepted answer

NA12878

My recommendation: download raw reads from Illumina BaseSpace and do alignment yourself. Aligning ~40X worth of human reads takes overnight with ~16 CPU cores.
You can acquire Platinum Genome data from ENA. 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, in particular this Word document. 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. 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?  

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