I'm downloading all valid dbSNPs from Biomart.org. I selected ensembl
variation 42, selected the "valid only" restriction, and left the
default attributes. If I click on XML in the navbar, I get a dataset
like
<Dataset name = "hsapiens_snp" interface = "default" >
<Attribute name = "chr_name" />
<Attribute name = "chrom_start" />
<Attribute name = "refsnp_id" />
<Filter name = "with_validated" excluded = "0"/>
</Dataset>
When I ask for a count, there are 5.6M, which is about what I got a few
months ago when I downloaded a slightly different version from ensembl.
However, when I do the actual download, I get only 1.9M lines. I
downloaded as tsv as well as xml.
Any thoughts?
-Amir Karger
