Repository 'plink'
hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/plink

Changeset 8:16d22eee0fe3 (2021-12-02)
Previous changeset 7:66b35562554d (2020-10-05) Next changeset 9:272aca44b3dd (2021-12-19)
Commit message:
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/plink commit b63133897598f2881de7bad1f18fcd69d7d7e9df"
modified:
plink.xml
test-data/out.assoc.fisher.adjusted
test-data/out.assoc.fisher.mperm
test-data/out.assoc.logistic.adjusted
b
diff -r 66b35562554d -r 16d22eee0fe3 plink.xml
--- a/plink.xml Mon Oct 05 16:08:24 2020 +0000
+++ b/plink.xml Thu Dec 02 16:20:30 2021 +0000
b
@@ -1,7 +1,7 @@
 <tool id='plink' name='plink' version='@TOOL_VERSION@+galaxy@VERSION_SUFFIX@'>
     <macros>
         <token name='@TOOL_VERSION@'>1.9.b618</token>
-        <token name='@VERSION_SUFFIX@'>2</token>
+        <token name='@VERSION_SUFFIX@'>3</token>
         <xml name='template_sanitizer'>
             <sanitizer>
                 <valid initial='default'>
@@ -38,6 +38,9 @@
             </sanitizer>
         </xml>
     </macros>
+    <xrefs>
+        <xref type="bio.tools">plink</xref>
+    </xrefs>
     <requirements>
         <requirement type='package' version='1.90b6.18'>plink</requirement>
     </requirements>
@@ -354,7 +357,7 @@
             $functions.logistic.beta
             $functions.logistic.intercept
         #end if
-
+        --lambda $functions.lambda
     #elif $functions.func == 'ibd':
         #if $functions.genome.output_genome:
             --genome
@@ -443,11 +446,11 @@
             <when value='filtering'>
                 <conditional name='id_list'>
                     <param name='func' type='select' label='ID list functions'>
-                        <option value='none'/>
-                        <option value='keep'/>
-                        <option value='keep-fam'/>
-                        <option value='remove'/>
-                        <option value='remove-fam'/>
+                        <option value='none'>None</option>
+                        <option value='keep'>Keep by sample IDs</option>
+                        <option value='keep-fam'>Keep by family IDs</option>
+                        <option value='remove'>Remove by sample IDs</option>
+                        <option value='remove-fam'>Remove by family IDs</option>
                     </param>
                     <when value='none'/>
                     <when value='keep'>
@@ -465,9 +468,9 @@
                 </conditional>
                 <conditional name='extraction'>
                     <param name='ex_func' type='select' label='ID extraction functions'>
-                        <option value='none'/>
-                        <option value='extract'/>
-                        <option value='exclude'/>
+                        <option value='none'>None</option>
+                        <option value='extract'>Keep by variant IDs</option>
+                        <option value='exclude'>Remove by variant IDs </option>
                     </param>
                     <when value='none'/>
                     <when value='extract'>
@@ -568,8 +571,8 @@
                 </conditional>
                 <conditional name='thinning'>
                     <param name='thinning' type='select' label='Arbitrary thinning'>
-                        <option value='No'/>
-                        <option value='Yes'/>
+                        <option value='No'>No</option>
+                        <option value='Yes'>Yes</option>
                     </param>
                     <when value='No'/>
                     <when value='Yes'>
@@ -620,8 +623,8 @@
                 </section>
                 <conditional name='hwe'>
                     <param  name='hwe' type='select' help='Set Hardy-Weinberg equilibrium tests'>
-                        <option value='No'/>
-                        <option value='Yes'/>
+                        <option value='No'>No</option>
+                        <option value='Yes'>Yes</option>
                     </param>
                     <when value='No'/>
                     <when value='Yes'>
@@ -637,8 +640,8 @@
                 </conditional>
                 <conditional name='sex_founder_filter'>
                     <param name='filter' type='select' label='Filter on sex and/or founders'>
-                        <option value='No'/>
-                        <option value='Yes'/>
+                        <option value='No'>No</option>
+                        <option value='Yes'>Yes</option>
                     </param>
                     <when value='No'/>
                     <when value='Yes'>
@@ -663,8 +666,8 @@
             <when value='data_manage'>
                 <conditional name='bmerge'>
                     <param name='set' type='select' label='Merge plink tilesets'>
-                        <option value='No'/>
-                        <option value='Yes'/>
+                        <option value='No'>No</option>
+                        <option value='Yes'>Yes</option>
                     </param>
                     <when value='No'/>
                     <when value='Yes'>
@@ -805,8 +808,8 @@
                 <param name='read_genome' label='Reusing an IBS/IBD calculation' format='tabular,tsv' type='data' optional='true'/>
                 <conditional name='cluster'>
                     <param name='cluster' type='select' help='Use IBS values calculated via --genome to perform complete linkage clustering'>
-                        <option value='No'/>
-                        <option value='Yes'/>
+                        <option value='No'>No</option>
+                        <option value='Yes'>Yes</option>
                     </param>
                     <when value='No'/>
                     <when value='Yes'>
@@ -817,8 +820,8 @@
                         </param>
                         <conditional name='mds'>
                             <param name='mds_scaling' type='select' help='Return a Haploview-friendly multidimensional scaling report'>
-                                <option value='No'/>
-                                <option value='Yes'/>
+                                <option value='No'>No</option>
+                                <option value='Yes'>Yes</option>
                             </param>
                             <when value='No'/>
                             <when value='Yes'>
@@ -837,7 +840,7 @@
                 <conditional name='assoc'>
                     <param name='assoc' label='Perform 1df chi-square allelic test' type='select'>
                         <option value=''>No</option>
-                        <option value='Yes'/>
+                        <option value='Yes'>Yes</option>
                     </param>
                     <when value=''/>
                     <when value='Yes'>
@@ -865,8 +868,8 @@
                 </conditional>
                 <conditional name='adjust'>
                     <param name='adjust' label='Report basic multiple testing corrections for the raw p-values' type='select'>
-                        <option value='No'/>
-                        <option value='Yes'/>
+                        <option value='No'>No</option>
+                        <option value='Yes'>Yes</option>
                     </param>
                     <when value='No'/>
                     <when value='Yes'>
@@ -921,8 +924,8 @@
                 </conditional> -->
                 <conditional name='logistic'>
                     <param name='logistic' type='select' label='Perform logistic regression and return report'>
-                        <option value='No'/>
-                        <option value='Yes'/>
+                        <option value='No'>No</option>
+                        <option value='Yes'>Yes</option>
                     </param>
                     <when value='No'/>
                     <when value='Yes'>
@@ -967,7 +970,7 @@
                 <conditional name='genome'>
                     <param name='output_genome' type='select' help='Perform and return results of IBS/IBD computation'>
                         <option value=''>No</option>
-                        <option value='Yes'/>
+                        <option value='Yes'>Yes</option>
                     </param>
                     <when value=''/>
                     <when value='Yes'>
@@ -1373,4 +1376,4 @@
     <citations>
         <citation type='doi'>10.1186/s13742-015-0047-8</citation>
     </citations>
-</tool>
\ No newline at end of file
+</tool>
b
diff -r 66b35562554d -r 16d22eee0fe3 test-data/out.assoc.fisher.adjusted
--- a/test-data/out.assoc.fisher.adjusted Mon Oct 05 16:08:24 2020 +0000
+++ b/test-data/out.assoc.fisher.adjusted Thu Dec 02 16:20:30 2021 +0000
b
b'@@ -1,51 +1,51 @@\n  CHR     SNP      UNADJ         GC         QQ       BONF       HOLM   SIDAK_SS   SIDAK_SD     FDR_BH     FDR_BY\n-   1   snp13      1.369      1.369          2          0          0    0.05171    0.05171    0.05883          0 \n-   1   snp45      1.276      1.276      1.523          0          0    0.02964    0.03136    0.05883          0 \n-   1   snp22      1.188      1.188      1.301          0          0    0.01545    0.01771    0.05883          0 \n-   1    snp1      1.019      1.019      1.155          0          0   0.002837   0.003842    0.05883          0 \n-   1    snp5     0.8623     0.8623      1.046          0          0  0.0002697   0.000487    0.05883          0 \n-   1   snp15     0.7893     0.7893     0.9586          0          0  6.152e-05  0.0001493    0.05883          0 \n-   1   snp33     0.7185     0.7185     0.8861          0          0   1.07e-05  3.822e-05    0.05883          0 \n-   1   snp36      0.717      0.717     0.8239          0          0  1.028e-05  3.822e-05    0.05883          0 \n-   1   snp21     0.6489     0.6489     0.7696          0          0  1.314e-06  1.004e-05    0.05883          0 \n-   1   snp18     0.6487     0.6487     0.7212          0          0  1.303e-06  1.004e-05    0.05883          0 \n-   1   snp23     0.5838     0.5838     0.6778          0          0  1.195e-07  2.452e-06    0.05883          0 \n-   1   snp12     0.5228     0.5228     0.6383          0          0  7.772e-09  3.935e-07    0.05883          0 \n-   1   snp41     0.5219     0.5219     0.6021          0          0  7.455e-09  3.935e-07    0.05883          0 \n-   1   snp17     0.4642     0.4642     0.5686          0          0  3.191e-10  7.563e-08    0.05883          0 \n-   1    snp2     0.4625     0.4625     0.5376          0          0  2.869e-10  7.563e-08    0.05883          0 \n-   1   snp35     0.4622     0.4622     0.5086          0          0  2.825e-10  7.563e-08    0.05883          0 \n-   1   snp28     0.4103     0.4103     0.4815          0          0  8.864e-12  2.336e-08    0.05883          0 \n-   1   snp38     0.4069     0.4069     0.4559          0          0  6.895e-12  2.336e-08    0.05883          0 \n-   1   snp43     0.4064     0.4064     0.4318          0          0  6.662e-12  2.336e-08    0.05883          0 \n-   1    snp8     0.4062     0.4062     0.4089          0          0  6.539e-12  2.336e-08    0.05883          0 \n-   1    snp9     0.3537     0.3537     0.3872          0          0  8.607e-14  1.038e-08    0.05883          0 \n-   1   snp19     0.3524     0.3524     0.3665          0          0  7.618e-14  1.038e-08    0.05883          0 \n-   1   snp44     0.3523     0.3523     0.3468          0          0  7.575e-14  1.038e-08    0.05883          0 \n-   1   snp31      0.352      0.352     0.3279          0          0  7.348e-14  1.038e-08    0.05883          0 \n-   1   snp29     0.3018     0.3018     0.3098          0          0  4.339e-16  6.787e-09    0.05883          0 \n-   1   snp30     0.3011     0.3011     0.2924          0          0  3.857e-16  6.787e-09    0.05883          0 \n-   1   snp42     0.3011     0.3011     0.2757          0          0  3.857e-16  6.787e-09    0.05883          0 \n-   1   snp49     0.3011     0.3011     0.2596          0          0  3.857e-16  6.787e-09    0.05883          0 \n-   1   snp34      0.253      0.253     0.2441          0          0          0  6.732e-09    0.05883          0 \n-   1   snp37     0.2529     0.2529     0.2291          0          0          0  6.732e-09    0.05883          0 \n-   1   snp40     0.2528     0.2528     0.2147          0          0          0  6.732e-09    0.05883          0 \n-   1   snp20     0.2526     0.2526     0.2007          0          0          0  6.732e-09    0.05883          0 \n-   1   snp48     0.2072     0.2072     0.1871          0          0          0  6.732e-09    0.05814          0 \n-   1   snp14      0.207      0.207     0.1739          0          0          0  6.732e-09    0.05814     '..b'      0 \n+   1   snp35     0.5296     0.5296     0.5086          0          0  1.082e-08  1.116e-06    0.09243          0 \n+   1   snp28     0.4689     0.4689     0.4815          0          0  4.225e-10  3.233e-07    0.09243          0 \n+   1   snp38      0.465      0.465     0.4559          0          0  3.334e-10  3.233e-07    0.09243          0 \n+   1   snp43     0.4644     0.4644     0.4318          0          0  3.228e-10  3.233e-07    0.09243          0 \n+   1    snp8     0.4641     0.4641     0.4089          0          0  3.171e-10  3.233e-07    0.09243          0 \n+   1    snp9     0.4031     0.4031     0.3872          0          0  5.202e-12  1.216e-07    0.09243          0 \n+   1   snp19     0.4016     0.4016     0.3665          0          0  4.628e-12  1.216e-07    0.09243          0 \n+   1   snp44     0.4015     0.4015     0.3468          0          0  4.604e-12  1.216e-07    0.09243          0 \n+   1   snp31     0.4011     0.4011     0.3279          0          0  4.473e-12  1.216e-07    0.09243          0 \n+   1   snp29      0.343      0.343     0.3098          0          0  3.158e-14  6.397e-08    0.09243          0 \n+   1   snp30     0.3422     0.3422     0.2924          0          0  2.917e-14  6.397e-08    0.09243          0 \n+   1   snp42     0.3422     0.3422     0.2757          0          0  2.917e-14  6.397e-08    0.09243          0 \n+   1   snp49     0.3422     0.3422     0.2596          0          0  2.917e-14  6.397e-08    0.09243          0 \n+   1   snp34     0.2867     0.2867     0.2441          0          0  4.822e-17  4.889e-08    0.09243          0 \n+   1   snp37     0.2866     0.2866     0.2291          0          0  4.822e-17  4.889e-08    0.09243          0 \n+   1   snp40     0.2864     0.2864     0.2147          0          0  4.822e-17  4.889e-08    0.09243          0 \n+   1   snp20     0.2862     0.2862     0.2007          0          0  4.822e-17  4.889e-08    0.09243          0 \n+   1   snp48      0.234      0.234     0.1871          0          0          0  4.889e-08    0.07281          0 \n+   1   snp14     0.2338     0.2338     0.1739          0          0          0  4.889e-08    0.07281          0 \n+   1    snp0      0.185      0.185     0.1612          0          0          0  1.905e-08    0.07281          0 \n+   1   snp11     0.1848     0.1848     0.1487          0          0          0  1.905e-08    0.07281          0 \n+   1    snp7     0.1845     0.1845     0.1367          0          0          0  1.905e-08    0.07281          0 \n+   1   snp26     0.1845     0.1845     0.1249          0          0          0  1.905e-08    0.07281          0 \n+   1   snp32     0.1386     0.1386     0.1135          0          0          0  1.905e-08    0.07281          0 \n+   1   snp16     0.1386     0.1386     0.1024          0          0          0  1.905e-08    0.07281          0 \n+   1   snp25     0.1384     0.1384    0.09151          0          0          0  1.905e-08    0.07281          0 \n+   1   snp39     0.1384     0.1384    0.08092          0          0          0  1.905e-08    0.07281          0 \n+   1   snp46     0.1383     0.1383    0.07058          0          0          0  1.905e-08    0.07281          0 \n+   1   snp47    0.09563    0.09563    0.06048          0          0          0  1.905e-08    0.06819          0 \n+   1    snp3    0.09519    0.09519    0.05061          0          0          0  1.905e-08    0.06819          0 \n+   1   snp27    0.09519    0.09519    0.04096          0          0          0  1.905e-08    0.06819          0 \n+   1    snp4    0.09506    0.09506    0.03152          0          0          0  1.905e-08    0.06819          0 \n+   1   snp24    0.05503    0.05503    0.02228          0          0          0  1.905e-08    0.03731          0 \n+   1    snp6    0.01765    0.01765    0.01323          0          0          0  1.905e-08    0.01759          0 \n+   1   snp10    0.01759    0.01759   0.004365          0          0          0  1.905e-08    0.01759          0 \n'
b
diff -r 66b35562554d -r 16d22eee0fe3 test-data/out.assoc.fisher.mperm
--- a/test-data/out.assoc.fisher.mperm Mon Oct 05 16:08:24 2020 +0000
+++ b/test-data/out.assoc.fisher.mperm Thu Dec 02 16:20:30 2021 +0000
b
@@ -1,51 +1,51 @@
  CHR     SNP         EMP1         EMP2 
-   1    snp0       0.6485            1 
-   1    snp1      0.06724       0.9756 
-   1    snp2       0.2894            1 
-   1    snp3       0.8024            1 
-   1    snp4       0.8102            1 
-   1    snp5      0.08614       0.9971 
+   1    snp0       0.6431            1 
+   1    snp1      0.06719       0.9733 
+   1    snp2       0.2927            1 
+   1    snp3       0.8004            1 
+   1    snp4       0.8184            1 
+   1    snp5      0.08444       0.9968 
    1    snp6       0.9608            1 
-   1    snp7       0.6315            1 
-   1    snp8       0.3596            1 
-   1    snp9       0.3878            1 
-   1   snp10       0.9566            1 
-   1   snp11       0.6523            1 
-   1   snp12       0.2271            1 
-   1   snp13      0.02575       0.7544 
-   1   snp14       0.5918            1 
-   1   snp15       0.1154       0.9996 
-   1   snp16       0.7294            1 
-   1   snp17        0.259            1 
-   1   snp18       0.1944            1 
-   1   snp19       0.3917            1 
-   1   snp20       0.5198            1 
-   1   snp21       0.1603            1 
-   1   snp22      0.03675       0.8985 
-   1   snp23       0.2278            1 
-   1   snp24       0.8825            1 
-   1   snp25       0.7269            1 
-   1   snp26       0.6533            1 
-   1   snp27       0.8142            1 
-   1   snp28       0.3383            1 
-   1   snp29       0.4681            1 
-   1   snp30        0.458            1 
-   1   snp31       0.3922            1 
-   1   snp32       0.7283            1 
-   1   snp33       0.1654       0.9999 
-   1   snp34       0.5148            1 
-   1   snp35       0.2918            1 
-   1   snp36        0.165       0.9999 
-   1   snp37       0.5271            1 
-   1   snp38       0.3427            1 
-   1   snp39       0.7368            1 
-   1   snp40       0.5179            1 
-   1   snp41        0.234            1 
-   1   snp42       0.4554            1 
-   1   snp43       0.3474            1 
-   1   snp44       0.4033            1 
-   1   snp45      0.02845       0.8325 
-   1   snp46       0.7231            1 
-   1   snp47       0.7953            1 
-   1   snp48       0.5771            1 
-   1   snp49       0.4793            1 
+   1    snp7       0.6308            1 
+   1    snp8       0.3555            1 
+   1    snp9       0.3804            1 
+   1   snp10       0.9594            1 
+   1   snp11       0.6511            1 
+   1   snp12       0.2293            1 
+   1   snp13      0.02615       0.7451 
+   1   snp14       0.5884            1 
+   1   snp15       0.1049       0.9996 
+   1   snp16        0.729            1 
+   1   snp17       0.2644            1 
+   1   snp18       0.2046            1 
+   1   snp19       0.3887            1 
+   1   snp20       0.5381            1 
+   1   snp21       0.1646            1 
+   1   snp22      0.03845       0.8917 
+   1   snp23        0.223            1 
+   1   snp24       0.8793            1 
+   1   snp25       0.7204            1 
+   1   snp26       0.6577            1 
+   1   snp27       0.8136            1 
+   1   snp28       0.3462            1 
+   1   snp29       0.4803            1 
+   1   snp30       0.4637            1 
+   1   snp31        0.402            1 
+   1   snp32       0.7339            1 
+   1   snp33       0.1639       0.9999 
+   1   snp34       0.5064            1 
+   1   snp35       0.2797            1 
+   1   snp36       0.1683       0.9999 
+   1   snp37       0.5299            1 
+   1   snp38       0.3401            1 
+   1   snp39       0.7348            1 
+   1   snp40       0.5115            1 
+   1   snp41       0.2287            1 
+   1   snp42       0.4542            1 
+   1   snp43       0.3372            1 
+   1   snp44       0.3965            1 
+   1   snp45        0.029       0.8276 
+   1   snp46       0.7211            1 
+   1   snp47       0.8059            1 
+   1   snp48       0.5881            1 
+   1   snp49       0.4842            1 
b
diff -r 66b35562554d -r 16d22eee0fe3 test-data/out.assoc.logistic.adjusted
--- a/test-data/out.assoc.logistic.adjusted Mon Oct 05 16:08:24 2020 +0000
+++ b/test-data/out.assoc.logistic.adjusted Thu Dec 02 16:20:30 2021 +0000
b
b'@@ -1,51 +1,51 @@\n  CHR     SNP      UNADJ         GC         QQ       BONF       HOLM   SIDAK_SS   SIDAK_SD     FDR_BH     FDR_BY\n-   1   snp13      1.206      1.206          2          0          0    0.01789    0.01789    0.07645          0 \n-   1   snp45      1.102      1.102      1.523          0          0    0.00711   0.007727    0.07645          0 \n-   1   snp17     0.9342     0.9342      1.301          0          0  0.0008958   0.001148    0.07645          0 \n-   1   snp22     0.8183     0.8183      1.155          0          0  0.0001145  0.0001877    0.07645          0 \n-   1   snp20     0.8014     0.8014      1.046          0          0  8.017e-05  0.0001595    0.07645          0 \n-   1   snp44     0.8006     0.8006     0.9586          0          0  7.882e-05  0.0001595    0.07645          0 \n-   1   snp36     0.7579     0.7579     0.8861          0          0  2.957e-05  9.353e-05    0.07645          0 \n-   1   snp31     0.6928     0.6928     0.8239          0          0  5.183e-06  2.534e-05    0.07645          0 \n-   1   snp15     0.6903     0.6903     0.7696          0          0  4.808e-06  2.534e-05    0.07645          0 \n-   1   snp48     0.6789     0.6789     0.7212          0          0  3.424e-06  2.534e-05    0.07645          0 \n-   1   snp33     0.6431     0.6431     0.6778          0          0  1.081e-06  1.427e-05    0.07645          0 \n-   1   snp21      0.603      0.603     0.6383          0          0  2.545e-07   5.98e-06    0.07645          0 \n-   1   snp12     0.5857     0.5857     0.6021          0          0  1.294e-07  4.766e-06    0.07645          0 \n-   1    snp1     0.5664     0.5664     0.5686          0          0  5.787e-08  3.548e-06    0.07645          0 \n-   1   snp38      0.556      0.556     0.5376          0          0  3.669e-08  3.508e-06    0.07645          0 \n-   1    snp5     0.4872     0.4872     0.5086          0          0  1.204e-09  4.444e-07    0.07645          0 \n-   1    snp3      0.481      0.481     0.4815          0          0  8.504e-10  4.444e-07    0.07645          0 \n-   1    snp8     0.4704     0.4704     0.4559          0          0  4.595e-10  4.444e-07    0.07645          0 \n-   1   snp32     0.4704     0.4704     0.4318          0          0  4.595e-10  4.444e-07    0.07645          0 \n-   1   snp18     0.4704     0.4704     0.4089          0          0  4.595e-10  4.444e-07    0.07645          0 \n-   1   snp40     0.3898     0.3898     0.3872          0          0  1.868e-12  6.575e-08    0.07645          0 \n-   1    snp2      0.384      0.384     0.3665          0          0  1.173e-12  6.575e-08    0.07645          0 \n-   1    snp4     0.3765     0.3765     0.3468          0          0  6.289e-13  6.575e-08    0.07645          0 \n-   1   snp35     0.3083     0.3083     0.3279          0          0  8.679e-16  5.034e-09    0.07645          0 \n-   1   snp26     0.3015     0.3015     0.3098          0          0  3.857e-16  5.034e-09    0.07645          0 \n-   1   snp42     0.3015     0.3015     0.2924          0          0  3.857e-16  5.034e-09    0.07645          0 \n-   1   snp43     0.2988     0.2988     0.2757          0          0  2.893e-16  5.034e-09    0.07645          0 \n-   1    snp0     0.2988     0.2988     0.2596          0          0  2.893e-16  5.034e-09    0.07645          0 \n-   1   snp14     0.2953     0.2953     0.2441          0          0  1.929e-16  5.034e-09    0.07645          0 \n-   1   snp28     0.2888     0.2888     0.2291          0          0  9.643e-17  5.034e-09    0.07645          0 \n-   1   snp39     0.2841     0.2841     0.2147          0          0  4.822e-17  5.034e-09    0.07645          0 \n-   1    snp6       0.23       0.23     0.2007          0          0          0  5.034e-09    0.06545          0 \n-   1   snp46     0.2257     0.2257     0.1871          0          0          0  5.034e-09    0.06545          0 \n-   1   snp25     0.2219     0.2219     0.1739          0          0          0  5.034e-09    0.06545     '..b'      0 \n+   1    snp5     0.5383     0.5383     0.5086          0          0  1.641e-08  2.766e-06     0.1215          0 \n+   1    snp3     0.5314     0.5314     0.4815          0          0  1.181e-08  2.766e-06     0.1215          0 \n+   1    snp8     0.5194     0.5194     0.4559          0          0  6.587e-09  2.766e-06     0.1215          0 \n+   1   snp32     0.5194     0.5194     0.4318          0          0  6.587e-09  2.766e-06     0.1215          0 \n+   1   snp18     0.5194     0.5194     0.4089          0          0  6.587e-09  2.766e-06     0.1215          0 \n+   1   snp40     0.4294     0.4294     0.3872          0          0  3.412e-11  3.758e-07     0.1039          0 \n+   1    snp2     0.4229     0.4229     0.3665          0          0   2.18e-11  3.758e-07     0.1039          0 \n+   1    snp4     0.4144     0.4144     0.3468          0          0  1.196e-11  3.758e-07     0.1039          0 \n+   1   snp35     0.3384     0.3384     0.3279          0          0  2.035e-14  2.753e-08     0.1039          0 \n+   1   snp26     0.3309     0.3309     0.3098          0          0  9.595e-15  2.753e-08     0.1039          0 \n+   1   snp42     0.3309     0.3309     0.2924          0          0  9.595e-15  2.753e-08     0.1039          0 \n+   1   snp43     0.3279     0.3279     0.2757          0          0  7.088e-15  2.753e-08     0.1039          0 \n+   1    snp0     0.3279     0.3279     0.2596          0          0  7.088e-15  2.753e-08     0.1039          0 \n+   1   snp14      0.324      0.324     0.2441          0          0  4.725e-15  2.753e-08     0.1039          0 \n+   1   snp28     0.3169     0.3169     0.2291          0          0  2.218e-15  2.753e-08     0.1039          0 \n+   1   snp39     0.3115     0.3115     0.2147          0          0  1.254e-15  2.753e-08     0.1039          0 \n+   1    snp6     0.2516     0.2516     0.2007          0          0          0  2.753e-08    0.08605          0 \n+   1   snp46     0.2469     0.2469     0.1871          0          0          0  2.753e-08    0.08605          0 \n+   1   snp25     0.2427     0.2427     0.1739          0          0          0  2.753e-08    0.08605          0 \n+   1   snp37      0.241      0.241     0.1612          0          0          0  2.753e-08    0.08605          0 \n+   1   snp41     0.1675     0.1675     0.1487          0          0          0  1.646e-08    0.06276          0 \n+   1   snp34     0.1638     0.1638     0.1367          0          0          0  1.646e-08    0.06276          0 \n+   1   snp19     0.1635     0.1635     0.1249          0          0          0  1.646e-08    0.06276          0 \n+   1   snp27     0.1631     0.1631     0.1135          0          0          0  1.646e-08    0.06276          0 \n+   1   snp30     0.1597     0.1597     0.1024          0          0          0  1.646e-08    0.06276          0 \n+   1   snp10    0.09339    0.09339    0.09151          0          0          0  1.646e-08    0.04525          0 \n+   1   snp24    0.09075    0.09075    0.08092          0          0          0  1.646e-08    0.04525          0 \n+   1   snp23    0.08824    0.08824    0.07058          0          0          0  1.646e-08    0.04525          0 \n+   1   snp16    0.08587    0.08587    0.06048          0          0          0  1.646e-08    0.04525          0 \n+   1   snp49    0.08361    0.08361    0.05061          0          0          0  1.646e-08    0.04525          0 \n+   1   snp29    0.08146    0.08146    0.04096          0          0          0  1.646e-08    0.04525          0 \n+   1   snp47    0.03328    0.03328    0.03152          0          0          0  1.646e-08     0.0254          0 \n+   1    snp7    0.02681    0.02681    0.02228          0          0          0  1.646e-08     0.0254          0 \n+   1    snp9     0.0254     0.0254    0.01323          0          0          0  1.646e-08     0.0254          0 \n+   1   snp11     0.0254     0.0254   0.004365          0          0          0  1.646e-08     0.0254          0 \n'