Importation of the new human genome build (hg38)

[robert....@griffith.edu.au]

I may have overlooked something in the IGV instructions, but I was wondering if anyone knowns a way to import the new hg38 build into IGV? My group has been doing some next-gen sequencing and we're having problems pinning down certain mutations because some of the genes have moved their base numbers since hg19.

Thanks in advance.

[Jim Robinson]

Hi Robert,

I'll try to get that up in the next few days.  In the meantime you can just download the fasta and load it yourself.   Its available from UCSC here:  http://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.fa.gz.  After downloading, gunzip and load it from the Genomes menu.   It will create an index the first time, which will take some time, let it finish.   You can download annotations from UCSC and other sources, the file we typically include by default is http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/refGene.txt.gz.   After loading the fasta you can load this from the File menu,  you don't need to gunzip it.

I may have overlooked something in the IGV instructions, but I was wondering if anyone knowns a way to import the new hg38 build into IGV? My group has been doing some next-gen sequencing and we're having problems pinning down certain mutations because some of the genes have moved their base numbers since hg19.

Thanks in advance.

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[James Robinson]

Hi Robert,

Apologies for the delayed response.  You can now download hg38 from our server  (Genomes > Load Genome from Server...").  Search for hg38.  As you are in Australlia you might get better performance if you also check "Download Sequence".  You will need about 3GB of local disk space if you use that option,  and the initial download might take a long time.

Jim

On Thu, Jul 10, 2014 at 3:31 AM, <robert....@griffith.edu.au> wrote:

I may have overlooked something in the IGV instructions, but I was wondering if anyone knowns a way to import the new hg38 build into IGV? My group has been doing some next-gen sequencing and we're having problems pinning down certain mutations because some of the genes have moved their base numbers since hg19.

Thanks in advance.

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