apraga/org - Change KG65Q3NYP36PHDD6PLGECRS736CI6YAL7OYTHFE6RGIR6KYCSFXAC

Mail paul

Created by Alexis Praga on November 8, 2023

KG65Q3NYP36PHDD6PLGECRS736CI6YAL7OYTHFE6RGIR6KYCSFXAC

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main

Change contents

Replacement in projects.org at line 52 [4.123895]

B:BD[3.140] → [3.140:184]

B:BD[3.184] → [5.15:43]

*** TODO Envoyer mail syndicat des internes
SCHEDULED: <2023-11-03 Fri>

[3.140]

[3.212]

*** DONE Envoyer mail syndicat des internes
CLOSED: [2023-11-08 Wed 19:03] SCHEDULED: <2023-11-03 Fri>

Replacement in projects.org at line 57 [4.123895]

B:BD[3.348] → [6.15:68]

*** TODO Mail rapporteur
SCHEDULED: <2023-11-06 Mon>

[3.348]

[6.68]

*** DONE Mail rapporteur
CLOSED: [2023-11-08 Wed 19:03] SCHEDULED: <2023-11-06 Mon>

Replacement in projects.org at line 61 [4.123895]

B:BD[7.270] → [7.270:332]

*** WAIT Assurance habitation
    SCHEDULED: <2023-11-12 Sun>

[7.270]

[7.332]

*** DONE Assurance habitation: envoyé
    CLOSED: [2023-11-08 Wed 19:19] SCHEDULED: <2023-11-12 Sun>

Insertion in projects.org at line 76 [4.123895]

[7.888]

[8.43]

*** KILL Attestation box ?
CLOSED: [2023-11-02 Thu 22:29] SCHEDULED: <2023-10-30 Mon>

Deletion in projects.org at line 213 [4.123895]

B:BD[9.1728] → [5.44:129]

** KILL Attestation box ?
CLOSED: [2023-11-02 Thu 22:29] SCHEDULED: <2023-10-30 Mon>

Replacement in projects.org at line 536 [4.123895]
∅:D[10.483] → [11.400:426]
B:BD[12.280] → [11.400:426]
B:BD[11.426] → [5.640:668]
```
*** TODO Corriger article
SCHEDULED: <2023-11-05 Sun>
```
[10.483]
[7.889]
```
*** DONE Corriger article
CLOSED: [2023-11-08 Wed 19:03] SCHEDULED: <2023-11-05 Sun>
```

Replacement in projects.org at line 949 [4.123895]

B:BD[13.539] → [7.1450:1511]

** TODO Payer facture eau Gennes
SCHEDULED: <2023-11-19 Sun>

[13.539]

[7.1511]

** WAIT Payer facture eau Gennes: à vérifier
SCHEDULED: <2023-11-09 Thu>
Payé 2023-11-08, à vérifier

Replacement in projects/bisonex.org at line 81 [14.35]

B:BD[2.8222] → [2.8222:9037]

∅:D[2.9037] → [15.16803:18186]

B:BD[16.8216] → [15.16803:18186]

gerized.csv | where "Found by bisonex" == "found" | where "Confirmed in sanger" == "true" | length
50
❯ open sangerized.csv | where "Found by bisonex" == "found" | where "Confirmed in sanger" == "" | length
71
❯ open sangerized.csv | where "Found by bisonex" == "missed" | where "Confirmed in sanger" == "" | length
5
❯ open sangerized.csv | where "Found by bisonex" == "missed" | where "Confirmed in sanger" == "true" | length
0
[[id:cd79a77c-a0b6-4bb1-9e08-fe08dc89e3aa][Résultats finaux]]
*** TODO Regarder 5 variants manqués
SCHEDULED: <2023-11-05 Sun>
open searched.csv |  where "Found by bisonex" == "missed"
A priori non confirmé sanger
*** DONE Refaire extraction
CLOSED: [2023-11-04 Sat 19:02] SCHEDULED: <2023-11-04 Sat>
*** DONE Refaire annotation avec mobidetails
CLOSED
: [2023-11-04 Sat 19:02] SCHEDULED: <2023-11-04 Sat>
*** DONE Refaire annotation avec transcrit non reconnus
CLOSED: [2023-11-04 Sat 20:42] SCHEDULED: <2023-11-04 Sat>
5 transcrits, donnés égalemen tpar
#+begin_src nu
open annotated.csv | where coding != "negatif" | where chrom == ""
#+end_src
| 62676048 | NM_001080420.1 | SHANK3    | référénce non valide   |
| 62690893 | NM_001080420.1 | KDM6B     | idem                   |
| 62690893 | NM_001080420.1 | KDM6B     | même variant           |
| 62795429 | NM_016381.3    | TREX1 | NM_033629.5   |
| 63019340 | NM_001080420.1 | SHANK3 | NM_001372044.2 |
SCHEDULED: <2023-11-01 Wed>
*** DONE Rajouter variant pour 63009152
CLOSED: [2023-11-04 Sat 20:47] SCHEDULED: <2023-11-01 Wed>
*** DONE Regénérer annotation avec NC_
CLOSED: [2023-11-04 Sat 18:59] SCHEDULED: <2023-10-31 Tue>
*** DONE Comparer variants manqué avec sanger: 0 confirmés
CLOSED: [2023-11-06 Mon 23:48] SCHEDULED: <2023-11-04 Sat>
*** TODO Annoter variants avec sanger
SCHEDULED: <2023-11-07 Tue>
*** TODO Mail paul avec résultats
SCHEDULED: <2023-11-05 Sun>
* Résultats
** TODO Speed-up BWA-mem
SCHEDULED: <2023-11-11 Sat>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-11-11 Sat>
* Communication
** DONE Mail NGS-diag
CLOSED: [2023-10-06 Fri 08:04] SCHEDULED: <2023-10-06 Fri>
/Entered on/ [2023-10-04 Wed 19:33]

[2.8222]

gerized.csv | where "Found by bisonex" == "found" | where "Confirmed in sanger" == "true" | length
50
❯ open sangerized.csv | where "Found by bisonex" == "found" | where "Confirmed in sanger" == "" | length
71
❯ open sangerized.csv | where "Found by bisonex" == "missed" | where "Confirmed in sanger" == "" | length
5
❯ open sangerized.csv | where "Found by bisonex" == "missed" | where "Confirmed in sanger" == "true" | length
0
[[id:cd79a77c-a0b6-4bb1-9e08-fe08dc89e3aa][Résultats finaux]]
*** DONE Regarder 5 variants manqués: 3 explicables, 2 non
CLOSED: [2023-11-09 Thu 00:22] SCHEDULED: <2023-11-05 Sun>
open searched.csv |  where "Found by bisonex" == "missed"
62982193  7884996 : haplotypecaller ok... -> filtré car AD=5 <= 10
63012582  102230760 : non présent haplotypcellar mais une délétion en 755 (en 754 CG -> C). Vérifié mobidetails
63019340  50721335 : non présent haplotypecaller (vérifié igv). vérifié mobidetails
63060439  26869324 : filtré car 15 reads
63109239  14358800 : présent haplotypecaller : filtré car DP=29 <= 30
Non présent haplotypecaller avec bcftools mais zgrep ok
zgrep 7884996 call_variant/haplotypecaller/*62982193*/*
zgrep 102230760 call_variant/haplotypecaller/*63012582*/*
zgrep 50721335 call_variant/haplotypecaller/*63019340*/*
zgrep 26869324 call_variant/haplotypecaller/*63060439*/*
zgrep 14358800 call_variant/haplotypecaller/*63109239*/*
*** DONE Flowchart
CLOSED: [2023-11-09 Thu 00:22]
*** DONE Refaire extraction
CLOSED: [2023-11-04 Sat 19:02] SCHEDULED: <2023-11-04 Sat>
*** DONE Refaire annotation avec mobidetails
CLOSED: [2023-11-04 Sat 19:02] SCHEDULED: <2023-11-04 Sat>
*** DONE Refaire annotation avec transcrit non reconnus
CLOSED: [2023-11-04 Sat 20:42] SCHEDULED: <2023-11-04 Sat>
5 transcrits, donnés égalemen tpar
#+begin_src nu
open annotated.csv | where coding != "negatif" | where chrom == ""
#+end_src
| 62676048 | NM_001080420.1 | SHANK3    | référénce non valide   |
| 62690893 | NM_001080420.1 | KDM6B     | idem                   |
| 62690893 | NM_001080420.1 | KDM6B     | même variant           |
| 62795429 | NM_016381.3    | TREX1 | NM_033629.5   |
| 63019340 | NM_001080420.1 | SHANK3 | NM_001372044.2 |
SCHEDULED: <2023-11-01 Wed>
*** DONE Rajouter variant pour 63009152
CLOSED: [2023-11-04 Sat 20:47] SCHEDULED: <2023-11-01 Wed>
*** DONE Regénérer annotation avec NC_
CLOSED: [2023-11-04 Sat 18:59] SCHEDULED: <2023-10-31 Tue>
*** DONE Comparer variants manqué avec sanger: 0 confirmés
CLOSED: [2023-11-06 Mon 23:48] SCHEDULED: <2023-11-04 Sat>
*** DONE Annoter variants avec sanger
CLOSED: [2023-11-08 Wed 23:17] SCHEDULED: <2023-11-07 Tue>
*** DONE Mail paul avec résultats
CLOSED: [2023-11-09 Thu 00:22] SCHEDULED: <2023-11-05 Sun>
* Résultats
** TODO Speed-up BWA-mem
SCHEDULED: <2023-11-11 Sat>
** TODO Speed-up Hapotypecaller
SCHEDULED: <2023-11-11 Sat>
* Communication
** DONE Mail NGS-diag
CLOSED: [2023-10-06 Fri 08:04] SCHEDULED: <2023-10-06 Fri>
/Entered on/ [2023-10-04 Wed 19:33]