apraga/org - Change RTP5CJJXW2DQQGKCS3R24GIB6MRCNVXWTZVUQYLXNNR4UXWWGD5AC

Bisonex : clinvar in dbsnp looks good

Created by Alexis Praga on November 27, 2022

RTP5CJJXW2DQQGKCS3R24GIB6MRCNVXWTZVUQYLXNNR4UXWWGD5AC

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Insertion in workout.org at line 5603 [4.1]

[3.219]

* Goals
Handstand + press handstand preparation 5min x2 par jour
* <2022-11-27 Sun> Handstand
 - Chest-to-wall 60s
 - Toe pull 12
 - Negative 5
 - Heel pull 10
 - L freestand 6

Replacement in projects.org at line 203 [4.123895]

B:BD[5.373] → [5.373:455]

***** TODO article T. Hirsch
***** TODO Autre case report NF1 + hépatoblastome ?

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[5.455]

***** DONE article T. Hirsch
CLOSED: [2022-11-27 Sun 11:28]
***** DONE Autre case report NF1 + hépatoblastome ?
CLOSED: [2022-11-27 Sun 11:28]

Replacement in projects.org at line 213 [4.123895]

∅:D[6.1384] → [5.822:873]

B:BD[5.822] → [5.822:873]

***** TODO NF1 + autres cancers
***** TODO Pathway

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***** DONE NF1 + autres cancers
CLOSED: [2022-11-27 Sun 11:28]
***** DONE Pathway
CLOSED: [2022-11-27 Sun 11:28]

Replacement in projects.org at line 253 [4.123895]
B:BD[8.1957] → [9.351:373]
```
**** TODO Poster v0.1
```
[8.1957]
[9.373]
```
**** DONE Poster v0.1
CLOSED: [2022-11-27 Sun 11:28]
```

Insertion in projects.org at line 256 [4.123895]

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**** TODO Soumission
- BMC Pediatrics ? Impact factor 2.1
  List journaux acceptant case reports
  https://static1.squarespace.com/static/5db7b349364ff063a6c58ab8/t/6071fb065173800a11ccd0a2/1618082566620/Case+Report+Journals+2020.pdf

Replacement in projects.org at line 1688 [4.123895]

B:BD[3.714] → [3.714:900]

On ne peut pas facilement vérifier qu'il n'y a pas de patho car chercher par position va renvoyer d'autres variants à cette position qui peuvent être patho.
  Ex:NC_000020.11 3234173

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On génère les positions à chercher dans clinvar.NB: je ne comprends pas pourquoi les régions ne fonctionne pas bien...  On fait juste un grep
#+begin_src sh :dir ~/code/bisonex/test_isec
# bcftools query -f '%CHROM\t%POS\t%POS\n' -i 'ID=@missing_id.txt' dbSNP_common_chr20.vcf.gz > to_search.txt
bcftools query -f '%POS\n' -i 'ID=@missing_id.txt' dbSNP_common_chr20.vcf.gz > to_search.txt
#+end_src
#+RESULTS:
Puis on regarde à la main les variations...
#+begin_src sh :dir ~/code/bisonex/test_isec
bcftools query -f '%POS %REF %ALT\ %INFO/CLNSIG\n' -i 'ID=@missing_id.txt' dbSNP_common_chr20.vcf.gz
bcftools query -f '%POS %REF %ALT %INFO/CLNSIG\n'  clinvar_chr20.vcf.gz | zgrep -f to_search.txt > to_check.txt
#+end_src
#+RESULTS:
| 3234173 T A    | C   | G . | . | . |  2 | 2 |   |   |   |   |
| 10658574 G A   | T . |   2 | 3 | 2 |  2 | 4 |   |   |   |   |
| 10672794 G A   | C . |   2 | 3 | 2 |  2 | 0 | 0 |   |   |   |
| 18525868 C T . | 0   |   2 |   |   |    |   |   |   |   |   |
| 25390747 G C . | 0   |     |   |   |    |   |   |   |   |   |
| 32800145 C G   | T . |   2 | 2 | 3 |  0 | 2 |   |   |   |   |
| 33412656 C G   | T . |   . | 2 | 2 |  0 | 2 |   |   |   |   |
| 45891622 G A   | C   | T . | . | 3 | 12 | 3 |   |   |   |   |
| 54171651 G A   | T . |  12 | 0 | 2 |    |   |   |   |   |   |
| 62172726 G A . | 0   |     |   |   |    |   |   |   |   |   |
| 63349782 G A   | C . |  11 | 2 | 2 |  2 | 0 |   |   |   |   |
| 63414925 G A   | C   | T . | 3 | 0 |  3 | 2 | 2 | 2 | 2 | . |
ON ne retrouve que des conflicting !

Replacement in projects.org at line 1763 [4.123895]
∅:D[2.1407] → [11.12:35]
∅:D[12.1432] → [11.12:35]
B:BD[13.100] → [11.12:35]
```
******* TODO Rtg tools
```
[2.1407]
[3.901]
```
******* HOLD Rtg tools
```