Reference genome UMD 3.1.1/bTau8 NOT WORKING

[Axel Villalobos]

Hello, until yesterday I was able to upload my bovine SNPs to the UMD 3.1.1/bTau8 reference genome, but today I can't see them. I updated to version 2.19.4 and can't see anything. Thank you.

[igv-help]

I'm not exactly sure what you mean. Can you be more specific about the steps you are taking and what the results are now vs when it was working for you.

Helga

[Axel Villalobos]

Thanks for the response. 

We have a 10,000 SNP database for cattle. The reference genome we use is UMD 3.1.1/BtAU8. When we upload our VCF file to the platform, the SNPs aren't visible. The same thing happens in the web version. These same files were previously viewable without any problems.

Axel Villalobos-Cortes

LABMA-IDIAP, AnGR and Biodiversity Research

Conbiand Network

REZGEN-IBA Network

ISAG-FAO Advisory Group

SNI-SENACYT Member

Yudansha Kai, APKS JKA/WF member

Yudansha Kai, Aikido Buikukiai member

Clayton CdS, BLG 221, Panamá

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[igv-help]

If you send us a section of your vcf file we can take a look. You can send it to us privately at igv-team at broadinstitute.org

[igv-help]

Could you check the sequence (chromosome) names in your VCF file and post the list, or a least a few, of the names here?

[Axel Villalobos]

i will send you a chr 6 in vcf

Axel Villalobos-Cortes

LABMA-IDIAP, AnGR and Biodiversity Research

Conbiand Network

REZGEN-IBA Network

ISAG-FAO Advisory Group

SNI-SENACYT Member

Yudansha Kai, APKS JKA/WF member

Yudansha Kai, Aikido Buikukiai member

Clayton CdS, BLG 221, Panamá

To view this discussion visit https://groups.google.com/d/msgid/igv-help/a4d14f88-52d6-46b2-ac7a-5a0e2634ec3dn%40googlegroups.com.

[James Robinson]

OK thanks, I see the issue.  The chromosome name is "6",  not "chr6".  We switched to UCSC alias files for chromosome names because in most cases they are more complete, and we do not have the resources to maintain these lists for the thousands of genomes we now support.  The UCSC alias list for BosTau8 is

chr6 GK000006.2 AC_000163.1

Note there are 2 aliases defined, but "6" is not one of them.  

As the "chrN <-> N" alias is an important special case I will work on a solution for the next release.    In the meantime a workaround that might work is to edit your "bosTau8.json" file in <user home>/igv/genomes and remove the following line

  "aliasURL": "https://hgdownload.soe.ucsc.edu/goldenPath/bosTau8/bigZips/bosTau8.chromAlias.txt",

This will cause IGV to use a default set of aliases which should work for your files.   Let us know here if that works.

Jim

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[Axel Villalobos]

Many thanks Jim!

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[James Robinson]

Yes, apologies for this.   Most genomes have "chr6-6" defined, I don't know why this one is different.    Will be fixed in the next release.

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[Axel Villalobos]

Hello James!

fixed! now we can se de SNP`s

thank you!

Axel Villalobos-Cortes

LABMA-IDIAP, AnGR and Biodiversity Research

Conbiand Network

REZGEN-IBA Network

ISAG-FAO Advisory Group

SNI-SENACYT Member

Yudansha Kai, APKS JKA/WF member

Yudansha Kai, Aikido Buikukiai member

Clayton CdS, BLG 221, Panamá

To view this discussion visit https://groups.google.com/d/msgid/igv-help/CACOP%2BptbAVOa-Keg--b51xT%2BXAc07iCL8ESWhV2OiuiJqw5-Fw%40mail.gmail.com.