dbSNP129 for hg19

[Jane M]

Hello,

As dbSNP129 is regarded as the last "clean" database, I am looking for it for hg19.
I could find only dbSNP131 here: ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/

Does someone know if it is possible to find this version, or at least dbSNP 130, for hg19?

Thank you in advance,
Jane

[shyam_la]

dbSNP129 for hg19 does not exist, atleast not from UCSC..

https://lists.soe.ucsc.edu/pipermail/genome/2009-May/019002.html

Probably because hg19 came after dbsnp130..

as to 130, it is possible it was removed from the UCSC website because it had issues with it

http://seqanswers.com/forums/showthread.php?t=6993

Though you should be able to able to find it somewhere, if you really want it!

[shyam_la]

ftp://ftp.broadinstitute.org/bundle/...ter_129.vcf.gz

You may want to use this from the GATK resource bundle..
They call it dbsnp135 excluding sites after 129, so essentially its 129..

[Jane M]

Thank you shyam_la!

I don't know why, I cannot access to ftp://ftp.broadinstitute.org/bundle/...ter_129.vcf.gz, but I have found dbsnp132, excluding sites after 129 here:

https://test.g2.bx.psu.edu/library_common/ldda_info?library_id=9c6348e21b1b5727&show_deleted=False&cntrller=library&folder_id=13866a76b20e769b&use_panels=False&id=b853402cd242cbb5

I will rather use this version than dbsnp131.

[shyam_la]

Try this:

Go to: ftp://[email protected]
Password: Blank

And then browse to bundle > 1.5 > hg19.

In any case, 132 excluding after 129 should be the same as this one..

[Jane M]

Perfect! Thanks