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espinos:results.primary.analysis.2 [2015/08/06 12:42] cespinos |
espinos:results.primary.analysis.2 [2016/06/24 15:51] (current) fgarcia |
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| === All unique variants detected === | === All unique variants detected === | ||
| - | {{:espinos:intersect_all_variants_bier_ssv5vscnag.png?410|}} | + | {{:espinos:images_ana:intersect_all_variants_bier_ssv5vscnag.png?410|}} |
| === Unique variants detected in neuropathies-related genes === | === Unique variants detected in neuropathies-related genes === | ||
| - | {{:espinos:intersect_genes_variants_bier_ssv5vscnag.png?410|}} | + | {{:espinos:images_ana:intersect_genes_variants_bier_ssv5vscnag.png?410|}} |
| === Summary by sample === | === 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 | ||
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| ^ Sample ^ N_var_BIER ^ N_var_neuropathies BIER ^ N_var_CNAG ^ N_var_neuropathies CNAG ^ N_var intersect ^ N_var_neuropathies intersect ^ | ^ Sample ^ N_var_BIER ^ N_var_neuropathies BIER ^ N_var_CNAG ^ N_var_neuropathies CNAG ^ N_var intersect ^ N_var_neuropathies intersect ^ | ||
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| - | ===== Variants metrics ===== | + | ===== Variants metrics by sample ===== |
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| + | * **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 === | === BIER's pipeline === | ||
| - | ^ Sample ^ N_total variants ^ N_hom ^ N_het ^ N_bialelic ^ N_multialelic ^ N_SNPs ^ N_indels ^ N_Ts ^ N_Tv ^ Ts_Tv Ratio ^ %_PASS ^ Mean quality ^ | + | ^ 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 | | | 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 | | | SGT077 | 53270 | 19025 | 34208 | 53233 | 37 | 50049 | 3221 | 35075 | 14995 | 2.34 | 95.22 | 573.19 | | ||
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| === CNAG's pipeline === | === CNAG's pipeline === | ||
| - | ^ Sample ^ N_total variants ^ N_hom ^ N_het ^ N_bialelic ^ N_SNPs ^ N_indels ^ N_Ts ^ N_Tv ^ Ts_Tv Ratio ^ %_PASS ^ Mean quality ^ | + | ^ 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 | | | 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 | | | SGT077 | 83416 | 31780 | 51636 | 83416 | 78111 | 5305 | 55679 | 22432 | 2,48 | 80,69 | 164,92 | | ||
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| | SGT241 | 79876 | 32252 | 47624 | 79876 | 74681 | 5195 | 53395 | 21286 | 2,51 | 82,12 | 170,69 | | | 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 | | | SGT274 | 84176 | 31984 | 52192 | 84176 | 78619 | 5557 | 55984 | 22635 | 2,47 | 82,21 | 168,49 | | ||
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