Question

Is There A Way To Use Broad Institute Snap Via Webservice Or Command Line ?

1

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12.8 years ago

Radhouane Aniba ▴ 790

Well my question is so clear that it fits only in the title :) SNAP is Here

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ADD COMMENT • link updated 12.8 years ago by Pierre Lindenbaum 161k • written 12.8 years ago by Radhouane Aniba ▴ 790

0

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PS : I am interested in SNAP Proxy Search

ADD REPLY • link 12.8 years ago by Radhouane Aniba ▴ 790

score 3 · Answer 1 · 2011-07-29

Yes, as far as I can see , their form accepts the simple POST data. So you can send a filled HTML form with curl:

$cat jeter2.txt

searchPairwise=&snpList=rs9627183%0D%0Ars11134178%0D%0Ars12915721%0D%0Ars2157697%0D%0Ars4011946%0D%0Ars6501530%0D%0Ars12301774%0D%0Ars2594278%0D%0Ars3792452+%0D%0Ars1065758%0D%0Ars12360508%0D%0Ars16847570%0D%0Ars175126%0D%0Ars933771&hapMapRelease=onekgpilot&hapMapPanel=CEU&RSquaredLimit=0.8&distanceLimit=500000&downloadType=File&includeQuerySnp=on&arrayFilter=query&columnList[]=DP&columnList[]=GP&columnList[]=AM&submit=search

$ curl -d @jeter2.txt "http://www.broadinstitute.org/mpg/snap/ldsearch.php"
SNP Proxy   Distance    RSquared    DPrime  Arrays  Chromosome  Coordinate_HG18
rs9627183   rs9627183   0   1.000   1.000   AN,A5,A6,AxM    chr22   46663178
rs9627183   rs80226347  172 0.826   1.000   None    chr22   46663350
rs9627183   rs77565490  350 0.826   1.000   None    chr22   46663528
rs9627183   rs9627184   374 0.826   1.000   AS,A5,A6,I6,IM,IMD,CYT,OQ,AxM,OE    chr22   46663552
rs9627183   rs738728    1477    0.826   1.000   AxM chr22   46664655
rs9627183   rs75377089  1936    0.826   1.000   None    chr22   46665114
rs9627183   rs9306505   2702    0.826   1.000   None    chr22   46660476
rs9627183   rs5768114   3423    0.826   1.000   A6,IM,IMD,OQ,OE chr22   46666601
rs11134178  rs11134178  0   1.000   1.000   AS,A6,IMD   chr5    6887167
rs11134178  rs11134179  309 1.000   1.000   AN,A6   chr5    6887476
rs11134178  rs62349472  690 1.000   1.000   None    chr5    6886477
rs11134178  rs62349474  783 1.000   1.000   None    chr5    6887950
rs11134178  rs62349475  828 1.000   1.000   None    chr5    6887995
rs11134178  rs11134180  1368    1.000   1.000   None    chr5    6888535
rs11134178  rs62349471  2099    1.000   1.000   None    chr5    6885068
rs11134178  rs12514681  4506    0.881   1.000   None    chr5    6882661
rs11134178  rs16878050  5739    0.881   1.000   None    chr5    6881428
rs11134178  rs62351788  6088    0.881   1.000   None    chr5    6881079
rs11134178  rs16878040  6302    0.881   1.000   None    chr5    6880865
rs11134178  rs62351787  7045    0.881   1.000   None    chr5    6880122
rs11134178  rs16878033  7353    0.881   1.000   None    chr5    6879814
rs11134178  rs16878029  7898    0.881   1.000   A6,CYT,OQ,AxM,OE    chr5    6879269
rs11134178  rs62351786  9087    0.881   1.000   None    chr5    6878080
rs11134178  rs62351785  11018   0.867   1.000   None    chr5    6876149
rs12915721  rs12915721  0   1.000   1.000   AN,A5,A6,CYT,OQ,OE  chr15   36138169
rs12915721  rs4923770   869 1.000   1.000   I3,I5,I6,I6Q,IM,IMD,IC,ICQ,OQ,IWQ,OE    chr15   36137300
rs12915721  rs12441437  5419    1.000   1.000   None    chr15   36143588
rs12915721  rs1587656   6205    1.000   1.000   AH,AxM  chr15   36131964
rs12915721  rs12899216  9143    1.000   1.000   None    chr15   36129026
rs12915721  rs11632429  9609    1.000   1.000   None    chr15   36128560
rs12915721  rs8024631   10752   1.000   1.000   I2,I5,I6,I6Q,IM,IMD,CM,IWQ  chr15   36148921
rs12915721  rs2088962   3035    0.831   1.000   None    chr15   36141204
rs12915721  rs931759    3251    0.831   1.000   None    chr15   36141420
rs12915721  rs12591780  4666    0.831   1.000   I6,IM,IMD   chr15   36142835
rs12915721  rs8023538   8549    0.831   1.000   None    chr15   36146718
rs12915721  rs12442242  10003   0.831   1.000   None    chr15   36128166
rs2157697   rs2157697   0   1.000   1.000   AS,A5,A6,IMD    chr17   9968291
rs2157697   rs3764428   2161    0.965   1.000   None    chr17   9966130
rs2157697   rs12449525  3844    0.836   1.000   IBC,AxM chr17   9964447
rs2157697   rs11653469  6237    0.836   1.000   None    chr17   9962054
rs2157697   rs739350    6525    0.836   1.000   None    chr17   9961766
rs2157697   rs739351    6690    0.836   1.000   None    chr17   9961601
rs2157697   rs56202505  1741    0.806   1.000   None    chr17   9966550
rs4011946   rs4011946   0   1.000   1.000   A6,CM   chr3    188679141
rs4011946   rs6444233   1565    1.000   1.000   None    chr3    188677576
rs4011946   rs2378265   5780    1.000   1.000   I3,I5,I6,I6Q,IM,IMD,IC,ICQ,OQ,IWQ,OE    chr3    188684921
rs4011946   rs1304543   9796    1.000   1.000   None    chr3    188688937
rs4011946   rs3096554   16482   1.000   1.000   I2,I5,I6,I6Q,IM,IMD,IWQ chr3    188695623
rs4011946   rs2553985   18506   1.000   1.000   None    chr3    188697647
rs4011946   rs2653306   21118   1.000   1.000   A6,AxM  chr3    188658023
rs4011946   rs1452186   21460   1.000   1.000   AN,A6,I1    chr3    188700601
rs4011946   rs9855124   22137   1.000   1.000   CYT,OQ,OE   chr3    188657004
rs4011946   rs2687929   2147    0.965   1.000   IMD chr3    188681288
rs4011946   rs7627176   6560    0.965   1.000   None    chr3    188672581
rs4011946   rs6444230   21801   0.965   1.000   AH,A6   chr3    188657340
rs4011946   rs2653308   24838   0.965   1.000   OQ  chr3    188654303
rs4011946   rs6780880   25464   0.965   1.000   None    chr3    188653677
rs4011946   rs2378267   9354    0.932   1.000   None    chr3    188688495
rs4011946   rs1579366   12060   0.932   1.000   None    chr3    188691201
rs4011946   rs1579367   12225   0.932   1.000   None    chr3    188691366
rs4011946   rs3096555   23670   0.932   1.000   None    chr3    188702811
rs4011946   rs2114123   12836   0.900   1.000   None    chr3    188691977
rs4011946   rs35846970  25637   0.900   1.000   None    chr3    188653504
rs4011946   rs7627192   24980   0.869   1.000   None    chr3    188654161
rs4011946   rs10460895  10810   0.840   1.000   AS,A5,A6    chr3    188689951
rs4011946   rs6807004   11736   0.840   1.000   I2,I5,I6,I6Q,IM,IMD,CYT,OQ,AxM,IWQ,OE   chr3    188690877
rs4011946   rs6807123   11843   0.840   1.000   None    chr3    188690984
rs4011946   rs7623274   14021   0.840   1.000   None    chr3    188693162
rs4011946   rs1579369   14358   0.840   1.000   None    chr3    188693499
rs4011946   rs2378268   15710   0.840   1.000   None    chr3    188694851
rs4011946   rs7613303   17311   0.840   1.000   None    chr3    188696452
rs4011946   rs9867986   18471   0.840   1.000   None    chr3    188697612
rs4011946   rs1823709   19219   0.840   1.000   None    chr3    188698360
rs4011946   rs13070379  20274   0.840   1.000   None    chr3    188699415
rs4011946   rs34408491  20705   0.840   1.000   None    chr3    188699846
rs4011946   rs12696575  20827   0.840   1.000   AN,A5,A6    chr3    188699968
rs4011946   rs17781342  21481   0.840   1.000   None    chr3    188700622
rs4011946   rs2653318   21994   0.840   1.000   A6,I2,I5,I6,I6Q,IM,IMD,IWQ  chr3    188701135
rs4011946   rs3115208   22808   0.840   1.000   None    chr3    188701949
rs4011946   rs3115210   23041   0.840   1.000   None    chr3    188702182
rs4011946   rs6771852   24330   0.840   1.000   AN,A5,A6    chr3    188703471
rs4011946   rs9820758   16433   0.812   1.000   A6  chr3    188662708
rs4011946   rs12696577  21162   0.812   1.000   None    chr3    188700303
rs4011946   rs2378240   22840   0.812   1.000   None    chr3    188656301
rs6501530   rs6501530   0   1.000   1.000   AS,A5,A6,AxM    chr17   67810758
rs6501530   rs7221883   2845    1.000   1.000   None    chr17   67807913
rs6501530   rs11652864  2898    1.000   1.000   AN,A5,A6    chr17   67807860
rs6501530   rs7217475   3021    1.000   1.000   None    chr17   67807737
rs6501530   rs1029644   3375    1.000   1.000   None    chr17   67807383
rs6501530   rs11653859  2858    0.967   1.000   None    chr17   67807900
rs6501530   rs1029645   3403    0.935   1.000   AS,A5,A6,I2,I5,I6,I6Q,IM,IMD,CYT,OQ,IWQ,OE  chr17   67807355
rs6501530   rs7211132   3435    0.935   1.000   None    chr17   67807323
rs6501530   rs11656920  28309   0.846   1.000   I6,IM,IMD,CYT,OQ,OE chr17   67782449
rs12301774  rs12301774  0   1.000   1.000   AS,A5,A6,IMD    chr12   114780495
rs2594278   rs2594278   0   1.000   1.000   A6,I2,I5,I6,I6Q,IM,IMD,IWQ  chr4    88080483
rs2594278   rs56232275  22830   0.869   1.000   None    chr4    88057653
rs2594278   rs112450884 22826   0.865   0.963   None    chr4    88057657
rs3792452   rs3792452   0   1.000   1.000   AN,A5,A6,I3,I5,I6,I6Q,IM,IMD,IC,ICQ,OQ,CM,IWQ   chr3    7641784
rs1065758   rs1065758   0   1.000   1.000   AN,A5,A6,I2,I5,I6,I6Q,IM,IMD,AxM,IWQ    chr21   37230781
rs12360508  rs12360508  0   1.000   1.000   A6  chr10   23260889
rs12360508  rs16922812  1187    0.915   1.000   OQ,OE   chr10   23262076
rs12360508  rs1171137   2819    0.915   1.000   None    chr10   23263708
rs12360508  rs2448132   4531    0.915   1.000   IMD,OQ,OE   chr10   23265420
rs12360508  rs3109068   4665    0.915   1.000   A6,I3,I5,I6,I6Q,IM,IMD,IC,ICQ,AxM,IWQ   chr10   23265554
rs12360508  rs3101796   4741    0.915   1.000   I6,IM,IMD   chr10   23265630
rs12360508  rs2464636   5101    0.915   1.000   None    chr10   23265990
rs12360508  rs1171138   2368    0.831   1.000   None    chr10   23263257
rs12360508  rs73600570  6109    0.831   1.000   None    chr10   23254780
rs12360508  rs7098947   6122    0.831   1.000   AG,CYT,OQ,AxM,OE    chr10   23254767
rs12360508  rs7094847   8942    0.831   1.000   I3,I5,I6,I6Q,IM,IMD,IC,ICQ,IWQ  chr10   23251947
rs12360508  rs12253561  13108   0.831   1.000   None    chr10   23247781
rs16847570  rs16847570  0   1.000   1.000   AS,A5,A6,OQ chr1    163839922
rs16847570  rs79321136  8734    1.000   1.000   None    chr1    163848656
rs16847570  rs12135169  9551    1.000   1.000   None    chr1    163849473
rs16847570  rs12133779  13518   1.000   1.000   None    chr1    163853440
rs16847570  rs76593835  41856   0.867   0.931   None    chr1    163798066
rs16847570  rs12125420  3367    0.866   1.000   AxM,OE  chr1    163843289
rs16847570  rs12128974  3852    0.866   1.000   I3,I5,I6,I6Q,IM,IMD,IC,ICQ,OQ,IWQ   chr1    163843774
rs16847570  rs7554080   7339    0.866   1.000   A6  chr1    163847261
rs16847570  rs12130157  12502   0.866   1.000   None    chr1    163852424
rs16847570  rs12142477  14513   0.866   1.000   None    chr1    163854435
rs16847570  rs1913836   17378   0.866   1.000   I3,I5,I6,I6Q,IM,IMD,IC,ICQ,OQ,IWQ,OE    chr1    163857300
rs175126    rs175126    0   1.000   1.000   AS,A5,A6,I1,IM,IMD,OQ,AxM,OE    chr11   60590200
rs175126    rs175127    89  0.967   1.000   None    chr11   60590289
rs175126    rs175125    313 0.935   1.000   None    chr11   60589887
rs175126    rs175129    1698    0.901   0.965   A6,I3,I5,I6,I6Q,IM,IMD,IC,ICQ,OQ,IWQ,OE chr11   60591898
rs933771    rs933771    0   1.000   1.000   A6,IM,IMD,CYT,OQ,OE chr15   93853488