Access Haploreg programmatically

Question

[zx8754]

Is it possible to submit a query to Haploreg programmatically (without using a browser) and get the output as text file?

I think Pierre Lindenbaum was asking the same question on Twitter...

.@yokofakun @notSoJunkDNA No cmd-line service, but I just put a VCF-formatted dump of the #haploreg database under the "Documentation" tab.

— Luke Ward (@Luke__Ward) June 7, 2013

[Pierre Lindenbaum]

there was a VCF file indexed with tabix. But I the download area seems to be "access denied" now. You should ask/tweet to @Luke_Ward

[zx8754]

Download in process at the moment. Presumable, I would need to calculate my LD from that VCF?

Answer 1

[lucas.d.ward]

Hi,

LD calculations are available along with the .vcf in the download directory in Haploreg v4.

Luke

[zx8754]

Could you share the code used to calculate LD from 1000 Genomes? Is it usual, download -> tabix -> plink pipeline? As I can see it is based on phase 1, I would like to recalculate using phase 3 for EUR population.