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[[espinos:dnanexus_variant]]
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A.2.3. Variant calling

For each VCF file, several statistical indicators about variant calling were calculated from VARIANT:

  • run: 4 runs were performed for this study. Run 1 included all 11 controls: patients with known mutations.
  • sampleID: ID for each sample.
  • N. variants: total number for each patient.
  • N. biallelic: total number of biallelic variants.
  • N. multiallelic: total number of multiallelic variants.
  • N. SNP: total number of Single Nucleotide Polymorphism for each patient.
  • N. indels: total number of Insertions or Deletions for each patient.
  • N. transit.: number of transitions.
  • N. transv.: number of transversions.
  • Ti/TV ratio: ratio between number of transitions and transversions.
  • Average quality: average quality for each sample.


run sampleID N. variants N. biallelic N. multiallelic N. SNP N. indels N. transit. N. transv. Ti/TV ratio Average q.
1 DNA_121 395 387 8 356 72 213 110 1.936 3928.593
1 DNA_554 383 375 8 338 62 207 112 1.848 4770.656
1 DNA_571 394 384 10 347 71 204 121 1.686 4010.143
1 DNA_708 392 385 7 356 75 208 107 1.944 4255.761
1 DNA_837 461 455 6 417 74 248 139 1.784 4428.973
1 DNA_872 431 423 8 395 70 226 135 1.674 4344.959
1 DNA-223 370 364 6 339 63 202 105 1.924 5149.503
1 DNA-621 383 376 7 345 68 202 114 1.772 4750.221
1 SGT-036 409 404 5 373 70 215 123 1.748 3935.444
1 SGT-044 400 391 9 354 76 217 106 2.047 4835.095
1 SGT-047 411 404 7 374 75 216 120 1.8 3813.728
2 1091 446 442 4 415 85 248 112 2.214 4534.759
2 1138 339 331 8 310 66 175 98 1.786 4813.04
2 1179 348 342 6 319 65 183 99 1.848 5259.841
2 SGT-006 407 400 7 380 71 214 121 1.769 4586.478
2 SGT-018 382 375 7 354 64 201 116 1.733 5128.584
2 SGT-027 381 374 7 351 69 193 118 1.636 4735.668
2 SGT-031 401 395 6 368 66 218 115 1.896 4635.239
2 SGT-034 444 435 9 404 79 243 125 1.944 4628.757
2 SGT-037 385 377 8 347 62 209 113 1.85 4656.921
2 SGT-093 396 388 8 360 77 213 105 2.029 4113.088
3 1133 400 394 6 364 73 212 115 1.843 4482.541
3 1175 358 350 8 317 64 180 114 1.579 5031.737
3 SGT-002 371 361 10 336 77 190 104 1.827 5657.693
3 SGT-019 363 354 9 324 62 189 112 1.688 4785.875
3 SGT-023 364 356 8 330 63 195 105 1.857 4971.326
3 SGT-029 405 395 10 369 72 220 114 1.93 4913.511
3 SGT-030 398 387 11 366 71 213 116 1.836 4977.476
3 SGT-056 398 393 5 355 71 222 105 2.114 4011.272
3 SGT-068 405 399 6 367 83 202 120 1.683 4846.31
3 SGT-072 383 378 5 341 67 203 112 1.812 4583.872
3 SGT-081 383 376 7 344 73 202 108 1.87 4408.119
4 DNA_1101 388 384 4 367 67 223 95 2.347 14297.886
4 SGT-105 383 379 4 364 59 221 101 2.188 17177.098
4 SGT-106 359 354 5 337 53 201 107 1.879 15052.651
4 SGT-109 333 327 6 316 61 186 84 2.214 18707.734
4 SGT-111 357 354 3 338 50 200 106 1.887 16106.623
4 SGT-113 397 390 7 372 68 221 106 2.085 15822.157
4 SGT-114 413 407 6 383 68 228 113 2.018 13528.107
4 SGT-139 380 371 9 357 59 211 108 1.954 14044.355
4 SGT-142 362 360 2 333 58 192 107 1.794 10913.104
4 SGT-169 355 350 5 336 48 215 90 2.389 16838.623
4 SGT-170 428 420 8 404 68 238 116 2.052 15184.186
espinos/dnanexus_variant.txt · Last modified: 2015/07/12 15:41 by fgarcia
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