====== 2.1 Primary Analysis - Variants comparison ======

===== Overview =====

=== All unique variants detected ===

{{:espinos:images_ana:intersect_all_variants_bier_ssv5vscnag.png?410|}}

=== Unique variants detected in neuropathies-related genes ===

{{:espinos:images_ana:intersect_genes_variants_bier_ssv5vscnag.png?410|}}

=== Summary by sample ===

  * **N_var**: number of total variants detected by each pipeline
  * **N_var_neuropathies**: number of variants detected by each pipeline found in neuropathies-related genes
  * **N_var intersect**: number of total variants detected by both pipelines
  * **N_var_neuropathies intersect**: number of variants detected by both pipelines and localised in neuropathies-related genes


^  Sample  ^  N_var_BIER  ^  N_var_neuropathies BIER  ^  N_var_CNAG  ^  N_var_neuropathies CNAG  ^  N_var intersect  ^  N_var_neuropathies intersect  ^
|  SGT038  |  53851  |  506  |  85942  |  902  |  42631  |  442  |  
|  SGT077  |  53230  |  487  |  83416  |  830  |  42191  |  415  |  
|  SGT161  |  52870  |  489  |  83533  |  866  |  42016  |  424  |  
|  SGT187  |  52320  |  539  |  84015  |  920  |  41339  |  459  |  
|  SGT230  |  52009  |  513  |  80023  |  854  |  41064  |  433  |  
|  SGT238  |  52960  |  526  |  82898  |  903  |  42230  |  466  |  
|  SGT241  |  52484  |  507  |  79876  |  863  |  41801  |  451  |  
|  SGT274  |  54182  |  473  |  84176  |  817  |  42885  |  410  |  


===== Variants metrics by sample =====

  * **N_total variants**: number of total variants detected by each pipeline
  * **N_hom**: number of homozygous variants (1/1) detected by each pipeline
  * **N_het**: number of heterozygous variants (0/1) detected by each pipeline
  * **N_biallelic**: number of variants with one alternative allele (0/1 or 1/1) detected by each pipeline
  * **N_multiallelic**: number of variants with more than one alternative allele (1/2) detected by BIER's pipeline
  * **N_SNPs**: number of Single Nucleotide Polymorphisms detected by each pipeline
  * **N_indels**: number of insertions or deletions detected by each pipeline
  * **N_Ts**: number of variants involving transitions (A↔G, C↔T) detected by each pipeline
  * **N_Tv**: number of variants involving transversions (A↔C, G↔T) detected by each pipeline
  * **Ts_Tv Ratio**: ratio between the number of transitions and transversions
  * **%_PASS**: percentage of variants tagged as "PASS" according to the parameters criteria assumed by each pipeline
  * **Mean quality**: mean quality of variants detected by each pipeline

=== BIER's pipeline ===

^  Sample  ^  N_total variants  ^ N_hom ^ N_het ^ N_biallelic ^  N_multiallelic  ^ N_SNPs ^ N_indels ^ N_Ts ^ N_Tv ^  Ts_Tv Ratio  ^ %_PASS ^  Mean quality  ^
|  SGT038  |  53851  |  19109  |  34686  |  53795  |  56  |  50431  |  3420  |  35362  |  15110  |  2.34  |  94.58  |  120283.15  |
|  SGT077  |  53270  |  19025  |  34208  |  53233  |  37  |  50049  |  3221  |  35075  |  14995  |  2.34  |  95.22  |  573.19  |
|  SGT161  |  52870  |  19235  |  33592  |  52827  |  43  |  49720  |  3150  |  34861  |  14899  |  2.34  |  94.92  |  590.80  |
|  SGT187  |  52320  |  19779  |  32500  |  52279  |  41  |  49080  |  3240  |  34375  |  14731  |  2.33  |  94.68  |  41671.02  |
|  SGT230  |  52009  |  20555  |  31414  |  51969  |  40  |  48668  |  3341  |  33942  |  14748  |  2.30  |  94.41  |  676.35  |
|  SGT238  |  52960  |  19927  |  32995  |  52922  |  38  |  49652  |  3308  |  34881  |  14798  |  2.36  |  94.95  |  632.60  |
|  SGT241  |  52484  |  19679  |  32767  |  52446  |  38  |  49234  |  3250  |  34591  |  14665  |  2.36  |  94.75  |  41551.44  |
|  SGT274  |  54182  |  18994  |  35141  |  54135  |  47  |  50730  |  3452  |  35491  |  15273  |  2.32  |  94.54  |  79919.49  |

=== CNAG's pipeline ===

^  Sample  ^  N_total variants  ^  N_hom  ^  N_het  ^  N_biallelic  ^  N_SNPs  ^  N_indels  ^  N_Ts  ^  N_Tv  ^  Ts_Tv Ratio  ^  %_PASS  ^  Mean quality  ^
|  SGT038  |  85942  |  33194  |  52748  |  85942  |  80248  |  5694  |  57382  |  22866  |  2,51  |  82,27  |  168,38  |
|  SGT077  |  83416  |  31780  |  51636  |  83416  |  78111  |  5305  |  55679  |  22432  |  2,48  |  80,69  |  164,92  |
|  SGT161  |  83533  |  32702  |  50831  |  83533  |  78187  |  5346  |  55675  |  22512  |  2,47  |  81,22  |  166,04  |
|  SGT187  |  84015  |  34875  |  49140  |  84015  |  78448  |  5567  |  55978  |  22470  |  2,49  |  81,47  |  167,02  |
|  SGT230  |  80023  |  34525  |  45498  |  80023  |  74659  |  5364  |  53070  |  21589  |  2,46  |  82,54  |  171,34  |
|  SGT238  |  82898  |  33457  |  49441  |  82898  |  77418  |  5480  |  55229  |  22189  |  2,49  |  81,94  |  168,63  |
|  SGT241  |  79876  |  32252  |  47624  |  79876  |  74681  |  5195  |  53395  |  21286  |  2,51  |  82,12  |  170,69  |
|  SGT274  |  84176  |  31984  |  52192  |  84176  |  78619  |  5557  |  55984  |  22635  |  2,47  |  82,21  |  168,49  |