apraga/org - Change 2PCPZD3BFBJXDOFKKSKVSPM7XZ7RQJQ3D7V7XD2C3ROEL5KDIICAC

Bisonex : tsv

Created by Alexis Praga on January 26, 2023

2PCPZD3BFBJXDOFKKSKVSPM7XZ7RQJQ3D7V7XD2C3ROEL5KDIICAC

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Insertion in projects/bisonex.org at line 8 [4.35]

[3.190]

*** Best practices for the analytical validation of clinical whole-genome sequencing intended for the diagnosis of germline disease
https://www.nature.com/articles/s41525-020-00154-9
Peu d’info sur la bionfo, sauf Supplementary :
Variant Type
|                       | SNVs & Indels | CNVs (>10Kb) | SVs | Mitochondrial variants | Pseudogenes | REs | Somatic/ mosaic | Literature/Data | Source   |
| NA12878               |         100%a |          40% |   0 |                      0 |           0 |   0 |               0 | Zook et  al18   | NIST     |
| Other NIST standard   |           71% |          40% | 50% |                      0 |           0 |   0 |               0 | Zook  et al18   |          |
| (e.g. AJ/Asian trios) |               |              |     |                        |             |     |                 |                 |          |
| Platinum              |           29% |            0 |   0 |                      0 |           0 |   0 |               0 | Eberle et  al8  | Platinum |
| Genomes               |               |              |     |                        |             |     |                 |                 |          |
| Venter/HuRef          |           14% |          40% |   0 |                      0 |           0 |   0 |               0 | Trost et al1    | HuRef    |

Insertion in projects/bisonex.org at line 25 [4.35]

[3.733]

[5.154]

*** Génerer des données de séquencage à partir de variant connu
https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-020-03665-5
1. génerer un modèle prenant en compte les biais d’Illumina
2. Génerer des fastq à partir de variants connus (ceux de centogène ??)
*** Vérifier les variants de centogene

Replacement in projects/bisonex.org at line 1272 [4.35]

B:BD[6.2109] → [6.2109:2140]

B:BD[6.2140] → [7.70:98]

*** TODO Comparer les versions
**** TODO bases de données

[6.2109]

[7.98]

*** DONE Comparer les versions
CLOSED: [2023-01-26 jeu. 17:42]
**** DONE bases de données
CLOSED: [2023-01-26 jeu. 17:42]

Replacement in projects/bisonex.org at line 1327 [4.35]

B:BD[6.2358] → [7.214:231]

**** TODO Outils

[6.2358]

[8.2697]

***** DONE Revérifer checksum de GRCh38 et dbSNP
CLOSED: [2023-01-26 jeu. 17:42]
****** DONE GRCh38
CLOSED: [2023-01-26 jeu. 17:42]
/Work/Projects/bisonex/data-alexis-reference/genome>sha256sum GRCh38_latest_genomic.fna
e0761a7ba5d10de9e7e97fa331667963925531c0199575bcceafbb13c3147e3f  GRCh38_latest_genomic.fna
PS J:\bases_de_donnees\genome> cat .\checksum.txt
e0761a7ba5d10de9e7e97fa331667963925531c0199575bcceafbb13c3147e3f  GRCh38_latest_genomic.fna
****** DONE dbSNP
CLOSED: [2023-01-26 jeu. 17:42]
/Work/Projects/bisonex/data-alexis-reference/dbSNP>sha256sum GCF_000001405.39.gz                 01/26/2023 04:40:48 PM
452e1112b6339a9b19821c2a226a8a3ba946e92a47e03e6ae464ef8820ee130d  GCF_000001405.39.gz
PS J:\bases_de_donnees\dbSNP> cat .\checksums.txt
452e1112b6339a9b19821c2a226a8a3ba946e92a47e03e6ae464ef8820ee130d  GCF_000001405.39.gz
**** DONE Outils
CLOSED: [2023-01-26 jeu. 17:42]

Insertion in projects/bisonex.org at line 1377 [4.35]

[9.1548]

[6.4283]

| tsv                 |       1087 |        1121 |             |             |            |            |            |

Replacement in projects/bisonex.org at line 2595 [4.35]
B:BD[2.16945] → [2.16945:16946]
[2.16945]
[8.96992]
```
***** TODO Regarder où sont les variants différents
```