Problems with snp142Common table

[Leo J. LEE]

Hi,

I downloaded the newly released common SNPs (142) track from the table browser and after a quick check, there seems to be some major issues:

1. The validation status of many SNPs are set to 'unknown', which is not consistent with the previous common SNPs track (141) or the NCBI dbSNP site. For example, rs575272151 at chr1:11008 is validated 'by 1000G, by frequency' according NCBI while listed as 'unknown' in the snp142Common table. rs75454623 at chr1:14930 is listed to be validated 'by-cluster,by-frequency' in the previous track and 'by 1000G,by frequency' at the NCBI site but 'unknown' in the current track. Since this is one of the fields that my script filters SNPs, it has a significant impact on my analysis.

2. Many SNPs from the previous track (141) seem to be gone. For example, rs180734498 at chr1:13302 is available when I search the NCBI site but not in the new track anymore.

Could somebody look into these and provide some explanations? Thanks a lot!

-- Leo

[Matthew Speir]

Hi Leo,

Thank you for bringing these issues with the new snp142Common table to our attention. We are working with dbSNP to resolve these issues. After we have resolved the issues, we will update the tracks and underlying tables. Thank you for your patience with this issue.

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

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[Ivan Adzhubey]

Hi Matthew,

Any updates regarding this issue? Looks like dbSNP has updated their VCFs for
build 142 at least twice since this February but UCSC download site only shows
the original (Feb 24) timestamps for snp142* files. Is a fix still in the works
or was it abandoned?

Thanks,
Ivan

Ivan Adzhubey, Ph.D.
Instructor
Division of Genetics, Dept of Medicine
Brigham & Women's Hospital
Harvard Medical School
New Research Building, Room 0464C
77 Avenue Louis Pasteur
Boston, MA 02115
tel.: (617) 525-4728
fax: (617) 525-4705
web: http://genetics.bwh.harvard.edu/wiki/sunyaevlab/

[Jonathan Casper]

Hello Ivan,

Thank you for checking up on this. The mid-April update to build 142 is something that we would like to incorporate, but at this point build 144 is likely to be released by the time that we would have the corrected version of 142 ready for display. The plan for now is that our next update will be for the release of SNP 144 data. We are keeping a close eye on the progress of 144 and may reconsider if it is significantly delayed.

If you have any further questions, please reply to gen...@soe.ucsc.edu or genome...@soe.ucsc.edu. Questions sent to those addresses will be archived in publicly-accessible forums for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

--
Jonathan Casper
UCSC Genome Bioinformatics Group

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