Good afternoon everyone, my name is Ben Busby and I am the genomics outreach coordinator
for NCBI. In the next 5 to 7 minutes I will show you four different ways to get data from
the Genome in a Bottle project.
With me, virutally, I have the head of the education group, Peter Cooper and Justin Zook,
a primary investigator at NIST who really spearheads the Genome in a Bottle project.
This consortium is a collaboration between NIST, FDA, NCBI and a whole bunch of other
people including volunteers to make data on which one can benchmark bioinformatics and
sequencing methodologies and look for regions with questionable variant calls and also to
identify high confidence variants.
In the next 5 to 7 minutes I will show you four ways to get the data and if you have
any questions please type them into the question pod.
One very quick way to get the data at NCBI is to go to the Genome in a Bottle BioProjects.
If we were to expand this out we would see a large abstract of what this is, and also
there is a link to the dedicated FTP site which I will show you at the end that has
the cutting edge Genome in a Bottle data as well as variant calls done by NIST and some
other groups.
The Genome in a Bottle data that is in BioProject and SRA currently has 13 BioSamples and when
you look at these here you see that some are from the 1000 genomes project and there are
other trios from other projects such as the PGP.
Also you can look at the SRA experiment associated with the Genome in a Bottle project. You can
see a list here. They are filterable using Entrez filtering, and when we filter we can
look at the aligned datasets such as the Complete Genomics dataset for the Ashkenazim Son. There
will be more aligned datasets coming into the SRA in the next few weeks.
When we click on the actual SRA run we can see the reference genome that it was aligned
to, the coverage and some other information about the alignment. If you are interested
in streaming aligned data, please check out the webinar we did on Feb 235. Also, unaligned
data and some aligned data can be investigated using SRA blast. We did a webinar on that
last November 5 and please feel free to check that out.
The other thing we can do with all of this data is investigate the metadata by sending
these projects to the SRA run selector. This run selector is SOLR-facetable resource where
one can look at available datasets that are in SRA for many BioSamples included in the
Genome in a Bottle project. There are many things that you can facet on. I've shown you
just a few that are faceting by BioSample and platform.
Here we can see that we can filter by just the Illumina and PacBio for one individual.
We can grab an accession list from that filtering and we can use this to loop over using the
sra-toolkit if we want to stream data, particularly parts of the genome or gene loci. These are
very useful, in my opinion, for benchmarking algorithms without downloading and mapping
the entire genome.
Another place one can get genotype calls from some of the Genome in a Bottle data, although
it is not necessarily a primary source of the Genome in a Bottle datam is from the GetRM
project. We have links here directly to some of the vcf and bed files produced by the NIST
group and there is also an associated FTP site where we see variant calls from a bunch
of different groups. The project also has a browser in which we can look at specific
genes and some of the variant calls.
I would just like to show you in the next 20 or 30 seconds some features of this browser.
You can see variant calls done by a number of different groups as well as a genotype
browser where you can see where the calls agree.
There is pretty good concordance between groups for most genomic regions.
The most authoritative place to get Genome in a Bottle data is from the Genome in a Bottle
FTP site. If you look at the README.ftp_structure there is an updated outline of where you can
get all of the data sets including recently updated data.
If you go a little bit farther into the data you can see data broken out by specific BioSamples
and by going into analysis one can go ahead and get the genotype calls for some of these
individuals.
One can get the latest data by going into ftp/release/*/latest/ and you can get calls
as well as bed files from that location.
If you'd like to get involved in this Genome in a Bottle project, some ways you could help
are by generating structural variants for any of the Ashkenazim trio and compare and integrate
those calls that you submit. You can compare and integrate phasing and also give feedback
as we see some of these high confidence calls.
If you are interested in getting involved you can contact me, BenBusby at nih.gov or
Justin.Zook at nist.gov.
With that what we would like to do is open the floor up to questions.
So, some people are having trouble accessing the trace website. And I have been asked to
restate it. The quickest way to find an accurate URL is to go to NCBI BioProjects, search for
Genome in a Bottle, find that BioProject and expand the abstract. ftp-trace.ncbi.nih.gov/giab/ftp/
Another question that I think is more appropriate for Justin is, are there any plans to liftover
to GRCh38?
That's a good question and we have talked a lot about this. Our plans are generally
to make calls on GRCh37 (hg19) first. We are working on methods to make calls on GRCh38
as well. We hope to have initial snp and indel calls in the next 4 to 6 months probably.
Those will probably be without using the Alt sequences initially, but we are interested
in using methods for the Alts.
Another person asks, what level of concordance do you generally expect to see now when looking
only at snps and short indels?
This really depends a lot on exactly what you are looking at. If you are looking in
the easier regions of the genome you can really see very close to 100% concordance as long
as you have good coverage. When you start getting to more difficult regions there is
often high discordance. Numbers that I often see if you take two different bioinformatics
algorithms or two different sequencing technologies then you have somewhere around 5 to 10% disagreement
between the two methods over the whole genome. If down select to the easier portions of the
genome, you can really have close to 100% concordance.
A more straightforward and fun question, have there been samples deposited from the X Ten
Illumina platform?
I don't think there have quite yet but I know some people have been generating these and
I believe there is an X Ten data set from the Garvan Institute that is available for
our pilot genome, NA12878. I think if you search for them you will be able to find them.
And just to make sure that they are not talking about the 10X platform, which is often confusing.
I think they actually do mean the X Ten Illumina platform. But the 10X data, 10
X Genomics, recently released data from NA12878 and the Ashkenazim trio. It's all available on
the FTP site.
All right, once again, if you have any other questions about things that we have covered
such as BioProjects or Alts, please free to check out our archived webinars, subscribe
to our YouTube channel or email me the questions or email questions to webinars at ncbi.nlm.nih.gov.
Thank you very much everybody and we will see you soon for other NCBI webinars.