apraga/org - Change ZJH3FM7YCDLERF3DF4AOPQS7C7SUZIOWTI5ZEPJBKKOFRHM7W4NAC

Bisonex

Created by Alexis Praga on March 9, 2023

ZJH3FM7YCDLERF3DF4AOPQS7C7SUZIOWTI5ZEPJBKKOFRHM7W4NAC

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main

Change contents

Insertion in workout.org at line 5979 [3.1]

[2.134]

* <2023-03-08 Wed> Workout
** Circuit
Haut: Muscle-up - Droit - L-sit - Tucked pushed - Muscle negative - tucked pull up - Skin-the-cat - Straddle negative
Bas: pistolsx4 - norwegian curlsx4 - extension x22s - compression x9
3x1

Replacement in projects/bisonex.org at line 3139 [6.35]

B:BD[4.1681] → [5.2478:2580]

***** TODO Bed donnés par GIAB (en hg19)
****** DONE résultats corrects
SCHEDULED: <2023-03-02 Thu>

[4.1681]

[7.3378]

***** DONE Bed donnés par GIAB (en hg19) : résultats corrects
CLOSED: [2023-03-09 Thu 22:42] SCHEDULED: <2023-03-02 Thu>

Replacement in projects/bisonex.org at line 3153 [6.35]

B:BD[7.4612] → [5.2581:3335]

***** TODO Comprendre pourquoi on est inférieur à Kumaran et al 2019
SCHEDULED: <2023-03-05 Sun>
****** TODO Comprende/améliorer Recall SNP 0.855
SCHEDULED: <2023-03-04 Sat>
******* TODO Regarder les FN (SNP)
SCHEDULED: <2023-03-04 Sat>
******** Manuel:
NC_000001.11:1385919 pas de read 1/1:FN:.:i1_5:INDEL:homalt:.
NC_000001.11:1623412 1 read     1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1668449 33 read sur 160 voient l'allèle alternative 1/1:FN:am:ti:SNP:homalt:.
NC_000001.11:1676135 67 reads, non vu 0/1:FN:.:ti:SNP:het:.
NC_000001.11:1734812 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1745808 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1745814 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1953616 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:2512975 0/1:FN:.:ti:SNP:het:

[7.4612]

[8.1338]


***** DONE Re-tester avec exons Refseq et option -T: résultats un peu moins bons
CLOSED: [2023-03-09 Thu 22:42] SCHEDULED: <2023-03-08 Wed>
On utilise directement les coordonées données par refseq

Replacement in projects/bisonex.org at line 3158 [6.35]

B:BD[8.1339] → [5.3336:3362]

******* TODO Statistiques

[8.1339]

[5.3362]

 Type Filter  TRUTH.TOTAL  TRUTH.TP  TRUTH.FN  QUERY.TOTAL  QUERY.FP  QUERY.UNK  FP.gt  FP.al  METRIC.Recall  METRIC.Precision
INDEL    ALL         7226      3417      3809         6978      1599       1918    228    353       0.472876          0.683992
  SNP    ALL        59052     37825     21227        43480      1913       3740    675     35       0.640537          0.951862
 METRIC.Frac_NA  METRIC.F1_Score  TRUTH.TOTAL.TiTv_ratio  QUERY.TOTAL.TiTv_ratio  TRUTH.TOTAL.het_hom_ratio  QUERY.TOTAL.het_hom_ratio
       0.274864         0.559171                     NaN                     NaN                   1.547733                   2.756151
       0.086017         0.765767                2.433271                2.350281                   1.575230                   1.492346
***** TODO D'où vient la différence ?
SCHEDULED: <2023-03-09 Thu>
****** TODO Statistiques

Replacement in projects/bisonex.org at line 3193 [6.35]

B:BD[5.4279] → [2.149:226]

******** DONE Répartition par chromosome: variable mais seul le 6 = hotspot

[5.4279]

[2.226]

******* DONE Répartition par chromosome: variable mais seul le 6 = hotspot

Replacement in projects/bisonex.org at line 3245 [6.35]

B:BD[2.1192] → [2.1192:1225]

******** Est-on dans des exons ?

[2.1192]

[5.4464]

******* DONE Reads en dehors des exons
CLOSED: [2023-03-09 Thu 22:43]

Replacement in projects/bisonex.org at line 3254 [6.35]

B:BD[2.1519] → [2.1519:1541]

using CSV, DataFrames

[2.1519]

[2.1541]

using CSV, DataFrames, Intervals
# Check the number of reads for each false negative (stored in count.csv)
# from hap.py output:
# awk '!/^#/ && $10~/:FN:/ && $11~/NOCALL/ && $10~/SNP/ {print $1":"$2"-"$2}' test-allchr.vcf  |  xargs -I {} sh -c 'echo -n {}";"; samtools view ../NA12878_NIST.b am {} | wc -l' > count.csv

Replacement in projects/bisonex.org at line 3263 [6.35]

B:BD[2.1699] → [2.1699:1776]

    transform!(f, :Column1 => ByRow(x -> string.(split(x, "-"))[2]) => :pos)

[2.1699]

[2.1776]

    transform!(f, :Column1 => ByRow(x -> parse(Int64, string.(split(x, "-"))[2])) => :pos)

Replacement in projects/bisonex.org at line 3276 [6.35]

B:BD[5.4507] → [2.2123:2153]

f = groupedCount("count.csv")

[5.4507]

[2.2153]

# Check is position x is in exons for chromosome chr
function isExon(x, exons, chr)
    # Remove duplicates
    exonsU = unique(exons[chr])
    res = transform(exonsU, :interval => ByRow(z -> x in z) => :check)
    # Result only found interval
    found = res[res.check,:].interval
    isempty(found) ? missing : first(found)
end
reads = groupedCount("../NA12878/happy/count.csv")

Replacement in projects/bisonex.org at line 3289 [6.35]

B:BD[2.2188] → [2.2188:2254]

g = 1
x = parse(Int64, f[g][1, :pos])
x in exons[g][1, :interval]

[2.2188]

[2.2254]

for g in range(1, size(reads)[1])
    local found
    found = transform(reads[g], :pos => ByRow(x -> isExon(x, exons, g)) => :exon)
    readsMissing = found[ismissing.(found.exon), :]
    # print("$(k.chrom):")
    print(g)
    print(": $(size(reads[g])[1]) reads, ")
    println("$(size(readsMissing)[1]) not in exons")
end

Replacement in projects/bisonex.org at line 3299 [6.35]

∅:D[2.2264] → [5.4507:4572]

B:BD[5.4507] → [5.4507:4572]

****** TODO Vérifier qu'il ne manque pas des exons (avec bam ?)

[2.2264]

[5.4572]

1: 448 reads, 64 not in exons
2: 307 reads, 47 not in exons
3: 228 reads, 37 not in exons
4: 175 reads, 28 not in exons
5: 237 reads, 38 not in exons
6: 1223 reads, 304 not in exons
7: 274 reads, 52 not in exons
8: 414 reads, 41 not in exons
9: 161 reads, 47 not in exons
10: 194 reads, 37 not in exons
11: 304 reads, 39 not in exons
12: 254 reads, 32 not in exons
13: 168 reads, 120 not in exons
14: 184 reads, 26 not in exons
15: 250 reads, 90 not in exons
16: 239 reads, 29 not in exons
17: 373 reads, 35 not in exons
18: 85 reads, 17 not in exons
19: 576 reads, 46 not in exons
20: 83 reads, 22 not in exons
21: 67 reads, 14 not in exons
22: 117 reads, 24 not in exons
******* TODO Comprendre/améliorer Recall SNP 0.855
SCHEDULED: <2023-03-04 Sat>
 on est inférieur à Kumaran et al 2019
******** TODO Regarder les FN (SNP)
SCHEDULED: <2023-03-04 Sat  >
********* Manuel:
NC_000001.11:1385919 pas de read 1/1:FN:.:i1_5:INDEL:homalt:.
NC_000001.11:1623412 1 read     1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1668449 33 read sur 160 voient l'allèle alternative 1/1:FN:am:ti:SNP:homalt:.
NC_000001.11:1676135 67 reads, non vu 0/1:FN:.:ti:SNP:het:.
NC_000001.11:1734812 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1745808 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1745814 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:1953616 1/1:FN:.:ti:SNP:homalt:.
NC_000001.11:2512975 0/1:FN:.:ti:SNP:het:
****** TODO Alignement
******* DONE Même genome: idem
CLOSED: [2023-03-09 Thu 23:13]
******** GHC38 + version alexis + exons refseq
 Type Filter  TRUTH.TOTAL  TRUTH.TP  TRUTH.FN  QUERY.TOTAL  QUERY.FP  QUERY.UNK  FP.gt  FP.al  METRIC.Recall  METRIC.Precision
INDEL    ALL         7226      3417      3809         6979      1599       1919    228    353       0.472876          0.683992
  SNP    ALL        59052     37827     21225        43483      1913       3741    676     35       0.640571          0.951865
 METRIC.Frac_NA  METRIC.F1_Score  TRUTH.TOTAL.TiTv_ratio  QUERY.TOTAL.TiTv_ratio  TRUTH.TOTAL.het_hom_ratio  QUERY.TOTAL.het_hom_ratio
       0.274968         0.559171                     NaN                     NaN                   1.547733                   2.756698
       0.086034         0.765792                2.433271                2.350254                   1.575230                   1.492375
******** GHC38.p13 + notre version alexis + exons refseq
 Type Filter  TRUTH.TOTAL  TRUTH.TP  TRUTH.FN  QUERY.TOTAL  QUERY.FP  QUERY.UNK  FP.gt  FP.al  METRIC.Recall  METRIC.Precision
INDEL    ALL         7226      3417      3809         6978      1599       1918    228    353       0.472876          0.683992
  SNP    ALL        59052     37825     21227        43480      1913       3740    675     35       0.640537          0.951862
 METRIC.Frac_NA  METRIC.F1_Score  TRUTH.TOTAL.TiTv_ratio  QUERY.TOTAL.TiTv_ratio  TRUTH.TOTAL.het_hom_ratio  QUERY.TOTAL.het_hom_ratio
       0.274864         0.559171                     NaN                     NaN                   1.547733                   2.756151
       0.086017         0.765767                2.433271                2.350281                   1.575230                   1.492346
****** DONE Vérifier si coordonnées génomiques (vcf)
CLOSED: [2023-03-09 Thu 23:05]
****** TODO Variant calling
******* TODO Désactiver dbSNP ???
****** TODO Définition des exons
******* TODO Vérifier qu'il ne manque pas des exons (avec bam ?)

Insertion in projects/bisonex.org at line 3366 [6.35]
[5.4600]
[5.4600]