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  1. {:FILTER {:DUPE {:Description "\"Duplicate assays position.\""},
  2. :FAIL_REF {:Description "\"Assay failed to map to reference.\""},
  3. :TRIALLELIC {:Description "\"Tri-allelic assay.\""},
  4. :ZCALL_DIFF {:Description "\"ZCALL_DIFF\""}},
  5. :FORMAT {:GT {:Number "1",
  6. :Type "String",
  7. :Description "\"Genotype\""},
  8. :IGC {:Number "1",
  9. :Type "Float",
  10. :Description "\"Illumina GenCall Confidence Score\""},
  11. :GTZ {:Number "1",
  12. :Type "String",
  13. :Description "\"zCall Genotype\""},
  14. :R {:Number "1",
  15. :Type "Float",
  16. :Description "\"Normalized R value\""},
  17. :NORMY {:Number "1",
  18. :Type "Float",
  19. :Description "\"Normalized Y intensity\""},
  20. :BAF {:Number "1",
  21. :Type "Float",
  22. :Description "\"B Allele Frequency\""},
  23. :LRR {:Number "1",
  24. :Type "Float",
  25. :Description "\"Log R Ratio\""},
  26. :GTA {:Number "1",
  27. :Type "String",
  28. :Description "\"Illumina Autocall Genotype\""},
  29. :THETA {:Number "1",
  30. :Type "Float",
  31. :Description "\"Normalized Theta value\""},
  32. :Y {:Number "1",
  33. :Type "Integer",
  34. :Description "\"Raw Y intensity\""},
  35. :NORMX {:Number "1",
  36. :Type "Float",
  37. :Description "\"Normalized X intensity\""},
  38. :X {:Number "1",
  39. :Type "Integer",
  40. :Description "\"Raw X intensity\""}},
  41. :INFO {:meanR_AB {:Number "1",
  42. :Type "Float",
  43. :Description "\"Mean of normalized R for AB cluster\""},
  44. :devY_AA {:Number "1",
  45. :Type "Float",
  46. :Description "\"Standard deviation of normalized Y for AA cluster\""},
  47. :zthresh_X {:Number "1",
  48. :Type "Float",
  49. :Description "\"zCall X threshold\""},
  50. :ILLUMINA_STRAND {:Number "1",
  51. :Type "String",
  52. :Description "\"Probe strand\""},
  53. :devX_BB {:Number "1",
  54. :Type "Float",
  55. :Description "\"Standard deviation of normalized X for BB cluster\""},
  56. :meanY_AA {:Number "1",
  57. :Type "Float",
  58. :Description "\"Mean of normalized Y for AA cluster\""},
  59. :AF {:Number "A",
  60. :Type "Float",
  61. :Description "\"Allele Frequency, for each ALT allele, in the same order as listed\""},
  62. :N_AA {:Number "1",
  63. :Type "Integer",
  64. :Description "\"Number of AA calls in training set\""},
  65. :BEADSET_ID {:Number "1",
  66. :Type "Integer",
  67. :Description "\"Bead set ID for normalization\""},
  68. :ALLELE_A {:Number "1",
  69. :Type "String",
  70. :Description "\"A allele\""},
  71. :PROBE_A {:Number "1",
  72. :Type "String",
  73. :Description "\"Probe base pair sequence\""},
  74. :meanTHETA_BB {:Number "1",
  75. :Type "Float",
  76. :Description "\"Mean of normalized THETA for BB cluster\""},
  77. :meanX_AA {:Number "1",
  78. :Type "Float",
  79. :Description "\"Mean of normalized X for AA cluster\""},
  80. :zthresh_Y {:Number "1",
  81. :Type "Float",
  82. :Description "\"zCall Y threshold\""},
  83. :devTHETA_AA {:Number "1",
  84. :Type "Float",
  85. :Description "\"Standard deviation of normalized THETA for AA cluster\""},
  86. :ILLUMINA_CHR {:Number "1",
  87. :Type "String",
  88. :Description "\"Chromosome in Illumina manifest\""},
  89. :meanY_AB {:Number "1",
  90. :Type "Float",
  91. :Description "\"Mean of normalized Y for AB cluster\""},
  92. :meanY_BB {:Number "1",
  93. :Type "Float",
  94. :Description "\"Mean of normalized Y for BB cluster\""},
  95. :PROBE_B {:Number "1",
  96. :Type "String",
  97. :Description "\"Probe base pair sequence; not missing for strand-ambiguous SNPs\""},
  98. :devX_AA {:Number "1",
  99. :Type "Float",
  100. :Description "\"Standard deviation of normalized X for AA cluster\""},
  101. :ILLUMINA_BUILD {:Number "1",
  102. :Type "String",
  103. :Description "\"Genome Build in Illumina manifest\""},
  104. :AN {:Number "1",
  105. :Type "Integer",
  106. :Description "\"Total number of alleles in called genotypes\""},
  107. :AC {:Number "A",
  108. :Type "Integer",
  109. :Description "\"Allele count in genotypes, for each ALT allele, in the same order as listed\""},
  110. :SOURCE {:Number "1",
  111. :Type "String",
  112. :Description "\"Probe source\""},
  113. :devR_AB {:Number "1",
  114. :Type "Float",
  115. :Description "\"Standard deviation of normalized R for AB cluster\""},
  116. :devY_BB {:Number "1",
  117. :Type "Float",
  118. :Description "\"Standard deviation of normalized Y for BB cluster\""},
  119. :ALLELE_B {:Number "1",
  120. :Type "String",
  121. :Description "\"B allele\""},
  122. :N_AB {:Number "1",
  123. :Type "Integer",
  124. :Description "\"Number of AB calls in training set\""},
  125. :devR_BB {:Number "1",
  126. :Type "Float",
  127. :Description "\"Standard deviation of normalized R for BB cluster\""},
  128. :ILLUMINA_POS {:Number "1",
  129. :Type "Integer",
  130. :Description "\"Position in Illumina manifest\""},
  131. :meanR_AA {:Number "1",
  132. :Type "Float",
  133. :Description "\"Mean of normalized R for AA cluster\""},
  134. :devTHETA_AB {:Number "1",
  135. :Type "Float",
  136. :Description "\"Standard deviation of normalized THETA for AB cluster\""},
  137. :GC_SCORE {:Number "1",
  138. :Type "Float",
  139. :Description "\"Gentrain Score\""},
  140. :devY_AB {:Number "1",
  141. :Type "Float",
  142. :Description "\"Standard deviation of normalized Y for AB cluster\""},
  143. :meanTHETA_AB {:Number "1",
  144. :Type "Float",
  145. :Description "\"Mean of normalized THETA for AB cluster\""},
  146. :meanTHETA_AA {:Number "1",
  147. :Type "Float",
  148. :Description "\"Mean of normalized THETA for AA cluster\""},
  149. :devX_AB {:Number "1",
  150. :Type "Float",
  151. :Description "\"Standard deviation of normalized X for AB cluster\""},
  152. :refSNP {:Number "1",
  153. :Type "String",
  154. :Description "\"dbSNP rs ID\""},
  155. :meanR_BB {:Number "1",
  156. :Type "Float",
  157. :Description "\"Mean of normalized R for BB cluster\""},
  158. :devR_AA {:Number "1",
  159. :Type "Float",
  160. :Description "\"Standard deviation of normalized R for AA cluster\""},
  161. :devTHETA_BB {:Number "1",
  162. :Type "Float",
  163. :Description "\"Standard deviation of normalized THETA for BB cluster\""},
  164. :meanX_BB {:Number "1",
  165. :Type "Float",
  166. :Description "\"Mean of normalized X for BB cluster\""},
  167. :N_BB {:Number "1",
  168. :Type "Integer",
  169. :Description "\"Number of BB calls in training set\""},
  170. :meanX_AB {:Number "1",
  171. :Type "Float",
  172. :Description "\"Mean of normalized X for AB cluster\""}},
  173. :contig {:GL000239.1 {:length "33824", :assembly "GRCh37"},
  174. :GL000214.1 {:length "137718", :assembly "GRCh37"},
  175. :14 {:length "107349540", :assembly "GRCh37"},
  176. :NC_007605 {:length "171823", :assembly "NC_007605.1"},
  177. :GL000204.1 {:length "81310", :assembly "GRCh37"},
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  224. :Y {:length "59373566", :assembly "GRCh37"},
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  239. :X {:length "155270560", :assembly "GRCh37"},
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