apraga/org - Change MMNJGZDL5JSLFC5DKMQ4O32UJE3OQJDCZAUO6QFH42AIAWN3HKZAC

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Created by Alexis Praga on May 31, 2023

MMNJGZDL5JSLFC5DKMQ4O32UJE3OQJDCZAUO6QFH42AIAWN3HKZAC

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main

Change contents

Replacement in projects/bisonex.org at line 45 [3.35]

B:BD[2.10512] → [2.10512:18704]

+ ".bai" }
    downloadGenome | indexGenome
    indexGenome.out.index | view
    addSNV(f, bam, bamIndex, downloadGenome.out, indexGenome.out.index, indexGenome.out.dict, indexGenome.out.fai)
}
#+end_src
****** DONE v1.3: Lancer le pipeline pour vérifier qu'on retrouve les variants
CLOSED: [2023-05-19 Fri 18:41] SCHEDULED: <2023-05-18 Thu>
****** HOLD Corrigier position pour avoir une bonne VAF
POS POS+1 VAF ALT
Attention, la base corrigée est à POS+1...
****** DONE Comparaison manuelle avec julia (VAF = 1...)
CLOSED: [2023-05-19 Fri 21:58]
552 found over 585
***** TODO del
***** TODO ins
*** TODO [[id:966a298c-948a-4694-a6f5-c326b1046a05][XAMscissors.jl]] :xamscissors:
**** TODO Test SNV
SCHEDULED: <2023-05-30 Tue>
***** DONE Phase 1 : chr22, VAF=1
CLOSED: [2023-05-29 Mon 15:36]
****** DONE 1 SNV  : ok !
CLOSED: [2023-05-20 Sat 19:35] SCHEDULED: <2023-05-20 Sat>
#+begin_src
 make run READS="tests/bamscissors/corrected_{1,2}.fq.gz"
Puis on lance le pipeline sur correct_1
- [X] Variant visible dans IGV
- [X] Variant visible après alignement
- [X] Variant visible après appel de variant
****** KILL Tester SNV chromosome 22
CLOSED: [2023-05-29 Mon 15:36] SCHEDULED: <2023-05-20 Sat>
***** DONE PHase 2 : chr22, VAF variable
****** DONE de nombreux reads sont perdus -> ok sur un SNV en alignant sur chromosome 22
CLOSED: [2023-05-29 Mon 15:38]
Problème dansr le BAM car sans les insertion
******* DONE Filtrer les reads sans pair : idem
CLOSED: [2023-05-23 Tue 00:01]
FOUND:Found 16662 unpaired mates
	at htsjdk.samtools.SAMUtils.processValidationError(SAMUtils.java:470)
	at picard.sam.SamToFastq.doWork(SamToFastq.java:224)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
ex: chr22:42213078
On essaie
samtools view ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135.bam NC_000022.11  -hf 0x2 -o 63003856_chr22.bam
Ne rale pas...
SCHEDULED: <2023-05-22 Mon>
******* DONE Problème de la conversion BAM -> fastq ?
CLOSED: [2023-05-24 Wed 23:19]
******** DONE Test bamtofastq sur le BAM originel: idem
CLOSED: [2023-05-23 Tue 01:16]
Dans ~/recherche/code/bisonex/Bamscissors.jl
samtools view ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135.bam NC_000022.11  -hf 0x2 -o 63003856_chr22.bam
On trie bien par nom de read
samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorted.bam
Conversion en fastq. Attention à bien prendre le *fichier trié* !
samtools bam2fq  -1 63003856_chr22_init1.fq.gz -2 63003856_chr22_init2.fq.gz  -n 63003856_chr22_sorted.bam
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 2592110 reads
On envoie sur le mésocentre
scp 63003856_chr22_init{1,2}.fq.gz meso:/Work/Users/apraga/bisonex/tests/bamscissors
On démarre un job avec 24 coeurs pour aller vite
srun -c 24 -p smp -t 1:00:00 --pty bash
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef 63003856_chr22_init1.fq.gz 63003856_chr22_init2.fq.gz | samtools sort -@24 -o output.bam -
Dans /home/alex/recherche/bisonex/code/BamScissors.jl/aligned
❯ scp meso:/Work/Users/apraga/bisonex/tests/bamscissors/output.bam*
******** DONE Avec samtools fastq
CLOSED: [2023-05-23 Tue 01:16]
samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorted.bam
samtools fastq 63003856_chr22_1.fq.gz -2 63003856_chr22_2.fq.gz -0 /dev/null -s /dev/null -o 63003856_chr22_sorted.bam
scp 63003856_chr22_{1,2}.fq.gz  meso:/Work/Users/apraga/bisonex/tests/bamscissors/
mesocentre
 bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef 63003856_chr22_1.fq.gz 63003856_chr22_2.fq.gz | samtools sort -@24 -o output.bam
 scp meso:/Work/Users/apraga/bisonex/tests/bamscissors/output.bam\* aligned/
******** DONE En rajoutant .fna dans le doserrie (+samtools fastq): idem
CLOSED: [2023-05-23 Tue 01:16]
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef* .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef* .
bwa mem -t 24 genomeRef 63003856_chr22_1.fq.gz 63003856_chr22_2.fq.gz | samtools sort -@24 -o output.bam
******** DONE Test picard : idem
CLOSED: [2023-05-23 Tue 01:16]
Dans bisonex/code/BamScissors.jl
❯ picard SamToFastq -I 63003856_chr22_sorted.bam -F testpicard1.fastq -F2 testpicard2.fastq
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef testpicard1.fastq.gz testpicard2.fastq.gz | samtools sort -@24 -o testpicard.bam -
******** DONE Il ne manque pas des reads dans les fastq :
CLOSED: [2023-05-23 Tue 01:26]
bisonex/code/BamScissors.jl on  bamscissors [!?] via ஃ v1.9.0
❯ samtools  flagstat aligned/output.bam
1306273 + 0 in total (QC-passed reads + QC-failed reads)
1296055 + 0 primary
0 + 0 secondary
10218 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
1304871 + 0 mapped (99.89% : N/A)
1294653 + 0 primary mapped (99.89% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
bisonex/code/BamScissors.jl on  bamscissors [!?] via ஃ v1.9.0
❯ samtools flagstat 63003856_chr22.bam
2609214 + 0 in total (QC-passed reads + QC-failed reads)
2592110 + 0 primary
0 + 0 secondary
17104 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
2609214 + 0 mapped (100.00% : N/A)
2592110 + 0 primary mapped (100.00% : N/A)
2592110 + 0 paired in sequencing
1296055 + 0 read1
1296055 + 0 read2
2592110 + 0 properly paired (100.00% : N/A)
2592110 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
❯ echo $(zcat 63003856_chr22_init2.fq.gz | wc -l)/4 | bc
1296055
bisonex/code/BamScissors.jl on  bamscissors [!?] via ஃ v1.9.0 took 2s
❯ echo $(zcat 63003856_chr22_init1.fq.gz | wc -l)/4 | bc
1296055
❯ samtools  flagstat 63003856_chr22_sorted.bam
2609214 + 0 in total (QC-passed reads + QC-failed reads)
2592110 + 0 primary
0 + 0 secondary
17104 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
2609214 + 0 mapped (100.00% : N/A)
2592110 + 0 primary mapped (100.00% : N/A)
2592110 + 0 paired in sequencing
1296055 + 0 read1
1296055 + 0 read2
2592110 + 0 properly paired (100.00% : N/A)
2592110 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
******** DONE Avec sort -O BAM idem
CLOSED: [2023-05-23 Tue 01:21]
******** DONE Singleton ou non mapped ? nonVirtPosition
CLOSED: [2023-05-23 Tue 01:22]
❯ samtools bam2fq  -1 63003856_chr22_init1.fq.gz -2 63003856_chr22_init2.fq.gz -0 both -s single.fq.gz  -n 63003856_chr22_sorted.bam
bisonex/code/BamScissors.jl on  bamscissors [!?] via ஃ v1.9.0
❯ wc -l 63003856_chr22_init* both single.fq.gz
   403540 63003856_chr22_init1.fq.gz
   404788 63003856_chr22_init2.fq.gz
        0 both
        0 single.fq.gz
   808328 total
******** Problème d'aligner car les reads sont bien dans le .fastq ?
Ex:
 zgrep "A00853:477:HMLWYDSX3:2:2624:2826:18630" 63003856_chr22_{1,2}.fq.gz
63003856_chr22_1.fq.gz:@A00853:477:HMLWYDSX3:2:2624:2826:18630
63003856_chr22_2.fq.gz:@A00853:477:HMLWYDSX3:2:2624:2826:18630
******* DONE Refaire la manip sur bam chr22 non modifié + mail Alexis
CLOSED: [2023-05-23 Tue 23:27]
[1]_samtools view ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135.bam NC_000022.11  -f 0x2 -o 63003856_chr22.bam
 Les reads sont bien tous mappé
samtools flagstat 63003856_chr22.bam
2609214 + 0 in total (QC-passed reads + QC-failed reads)
2592110 + 0 primary
0 + 0 secondary
17104 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
2609214 + 0 mapped (100.00% : N/A)
[2] samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorte

[2.10512]

[2.18704]

+ ".bai" }
    downloadGenome | indexGenome
    indexGenome.out.index | view
    addSNV(f, bam, bamIndex, downloadGenome.out, indexGenome.out.index, indexGenome.out.dict, indexGenome.out.fai)
}
#+end_src
****** DONE v1.3: Lancer le pipeline pour vérifier qu'on retrouve les variants
CLOSED: [2023-05-19 Fri 18:41] SCHEDULED: <2023-05-18 Thu>
****** HOLD Corrigier position pour avoir une bonne VAF
POS POS+1 VAF ALT
Attention, la base corrigée est à POS+1...
****** DONE Comparaison manuelle avec julia (VAF = 1...)
CLOSED: [2023-05-19 Fri 21:58]
552 found over 585
***** TODO del
***** TODO ins
*** TODO [[id:966a298c-948a-4694-a6f5-c326b1046a05][XAMscissors.jl]] :xamscissors:
**** TODO Test SNV
SCHEDULED: <2023-05-30 Tue>
***** DONE Phase 1 : chr22, VAF=1
CLOSED: [2023-05-29 Mon 15:36]
****** DONE 1 SNV  : ok !
CLOSED: [2023-05-20 Sat 19:35] SCHEDULED: <2023-05-20 Sat>
#+begin_src
 make run READS="tests/bamscissors/corrected_{1,2}.fq.gz"
Puis on lance le pipeline sur correct_1
- [X] Variant visible dans IGV
- [X] Variant visible après alignement
- [X] Variant visible après appel de variant
****** KILL Tester SNV chromosome 22
CLOSED: [2023-05-29 Mon 15:36] SCHEDULED: <2023-05-20 Sat>
***** TODO PHase 2 : chr22, VAF variable
****** DONE de nombreux reads sont perdus -> ok sur un SNV en alignant sur chromosome 22
CLOSED: [2023-05-29 Mon 15:38]
Problème dansr le BAM car sans les insertion
******* DONE Filtrer les reads sans pair : idem
CLOSED: [2023-05-23 Tue 00:01]
FOUND:Found 16662 unpaired mates
	at htsjdk.samtools.SAMUtils.processValidationError(SAMUtils.java:470)
	at picard.sam.SamToFastq.doWork(SamToFastq.java:224)
	at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:308)
	at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:103)
	at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:113)
ex: chr22:42213078
On essaie
samtools view ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135.bam NC_000022.11  -hf 0x2 -o 63003856_chr22.bam
Ne rale pas...
SCHEDULED: <2023-05-22 Mon>
******* DONE Problème de la conversion BAM -> fastq ?
CLOSED: [2023-05-24 Wed 23:19]
******** DONE Test bamtofastq sur le BAM originel: idem
CLOSED: [2023-05-23 Tue 01:16]
Dans ~/recherche/code/bisonex/Bamscissors.jl
samtools view ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135.bam NC_000022.11  -hf 0x2 -o 63003856_chr22.bam
On trie bien par nom de read
samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorted.bam
Conversion en fastq. Attention à bien prendre le *fichier trié* !
samtools bam2fq  -1 63003856_chr22_init1.fq.gz -2 63003856_chr22_init2.fq.gz  -n 63003856_chr22_sorted.bam
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 2592110 reads
On envoie sur le mésocentre
scp 63003856_chr22_init{1,2}.fq.gz meso:/Work/Users/apraga/bisonex/tests/bamscissors
On démarre un job avec 24 coeurs pour aller vite
srun -c 24 -p smp -t 1:00:00 --pty bash
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef 63003856_chr22_init1.fq.gz 63003856_chr22_init2.fq.gz | samtools sort -@24 -o output.bam -
Dans /home/alex/recherche/bisonex/code/BamScissors.jl/aligned
❯ scp meso:/Work/Users/apraga/bisonex/tests/bamscissors/output.bam*
******** DONE Avec samtools fastq
CLOSED: [2023-05-23 Tue 01:16]
samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorted.bam
samtools fastq 63003856_chr22_1.fq.gz -2 63003856_chr22_2.fq.gz -0 /dev/null -s /dev/null -o 63003856_chr22_sorted.bam
scp 63003856_chr22_{1,2}.fq.gz  meso:/Work/Users/apraga/bisonex/tests/bamscissors/
mesocentre
 bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef 63003856_chr22_1.fq.gz 63003856_chr22_2.fq.gz | samtools sort -@24 -o output.bam
 scp meso:/Work/Users/apraga/bisonex/tests/bamscissors/output.bam\* aligned/
******** DONE En rajoutant .fna dans le doserrie (+samtools fastq): idem
CLOSED: [2023-05-23 Tue 01:16]
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef* .
ln -s /Work/Projects/bisonex/data/genome/GRCh38.p13/genomeRef* .
bwa mem -t 24 genomeRef 63003856_chr22_1.fq.gz 63003856_chr22_2.fq.gz | samtools sort -@24 -o output.bam
******** DONE Test picard : idem
CLOSED: [2023-05-23 Tue 01:16]
Dans bisonex/code/BamScissors.jl
❯ picard SamToFastq -I 63003856_chr22_sorted.bam -F testpicard1.fastq -F2 testpicard2.fastq
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/bwa/genomeRef testpicard1.fastq.gz testpicard2.fastq.gz | samtools sort -@24 -o testpicard.bam -
******** DONE Il ne manque pas des reads dans les fastq :
CLOSED: [2023-05-23 Tue 01:26]
bisonex/code/BamScissors.jl on  bamscissors [!?] via ஃ v1.9.0
❯ samtools  flagstat aligned/output.bam
1306273 + 0 in total (QC-passed reads + QC-failed reads)
1296055 + 0 primary
0 + 0 secondary
10218 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
1304871 + 0 mapped (99.89% : N/A)
1294653 + 0 primary mapped (99.89% : N/A)
0 + 0 paired in sequencing
0 + 0 read1
0 + 0 read2
0 + 0 properly paired (N/A : N/A)
0 + 0 with itself and mate mapped
0 + 0 singletons (N/A : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
bisonex/code/BamScissors.jl on  bamscissors [!?] via ஃ v1.9.0
❯ samtools flagstat 63003856_chr22.bam
2609214 + 0 in total (QC-passed reads + QC-failed reads)
2592110 + 0 primary
0 + 0 secondary
17104 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
2609214 + 0 mapped (100.00% : N/A)
2592110 + 0 primary mapped (100.00% : N/A)
2592110 + 0 paired in sequencing
1296055 + 0 read1
1296055 + 0 read2
2592110 + 0 properly paired (100.00% : N/A)
2592110 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
❯ echo $(zcat 63003856_chr22_init2.fq.gz | wc -l)/4 | bc
1296055
bisonex/code/BamScissors.jl on  bamscissors [!?] via ஃ v1.9.0 took 2s
❯ echo $(zcat 63003856_chr22_init1.fq.gz | wc -l)/4 | bc
1296055
❯ samtools  flagstat 63003856_chr22_sorted.bam
2609214 + 0 in total (QC-passed reads + QC-failed reads)
2592110 + 0 primary
0 + 0 secondary
17104 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
2609214 + 0 mapped (100.00% : N/A)
2592110 + 0 primary mapped (100.00% : N/A)
2592110 + 0 paired in sequencing
1296055 + 0 read1
1296055 + 0 read2
2592110 + 0 properly paired (100.00% : N/A)
2592110 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
******** DONE Avec sort -O BAM idem
CLOSED: [2023-05-23 Tue 01:21]
******** DONE Singleton ou non mapped ? nonVirtPosition
CLOSED: [2023-05-23 Tue 01:22]
❯ samtools bam2fq  -1 63003856_chr22_init1.fq.gz -2 63003856_chr22_init2.fq.gz -0 both -s single.fq.gz  -n 63003856_chr22_sorted.bam
bisonex/code/BamScissors.jl on  bamscissors [!?] via ஃ v1.9.0
❯ wc -l 63003856_chr22_init* both single.fq.gz
   403540 63003856_chr22_init1.fq.gz
   404788 63003856_chr22_init2.fq.gz
        0 both
        0 single.fq.gz
   808328 total
******** Problème d'aligner car les reads sont bien dans le .fastq ?
Ex:
 zgrep "A00853:477:HMLWYDSX3:2:2624:2826:18630" 63003856_chr22_{1,2}.fq.gz
63003856_chr22_1.fq.gz:@A00853:477:HMLWYDSX3:2:2624:2826:18630
63003856_chr22_2.fq.gz:@A00853:477:HMLWYDSX3:2:2624:2826:18630
******* DONE Refaire la manip sur bam chr22 non modifié + mail Alexis
CLOSED: [2023-05-23 Tue 23:27]
[1]_samtools view ~/code/bisonex/out/63003856/preprocessing/mapped/63003856_S135.bam NC_000022.11  -f 0x2 -o 63003856_chr22.bam
 Les reads sont bien tous mappé
samtools flagstat 63003856_chr22.bam
2609214 + 0 in total (QC-passed reads + QC-failed reads)
2592110 + 0 primary
0 + 0 secondary
17104 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
2609214 + 0 mapped (100.00% : N/A)
[2] samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorte

Replacement in projects/bisonex.org at line 47 [3.35]

B:BD[2.26896] → [2.26896:34531]

CDEECBDBCECBEECCEACDEEBBFGDEFGCCFFFFCFCCEFBFDCFCDAAEBEE:CECBABBEBEE;DBFCCCDBCDBCCBBC?@BEEDA	NM:i:0	MD:Z:151	MC:Z:151M	AS:i:151	XS:i:151	RG:Z:sample
Effectivement, on aligne sur une zonne supprimée !
******* DONE Corriger la qualité: non
CLOSED: [2023-05-24 Wed 22:19]
******** DONE Comparaison avec le fastq de référénce : qualité !!
CLOSED: [2023-05-24 Wed 22:17]
#+begin_src sh
cd /Work/Users/apraga/bisonex/work/6e/8548fc90263830bf677f36585f11dc
zgrep -A 3 "A00853:477:HMLWYDSX3:1:1413:4390:28573" 63003856_chr22_1.fq.gz
#+end_src
@A00853:477:HMLWYDSX3:1:1413:4390:28573
AGGGTTACCACCACCACCCTGACAGGAGATATTCTAGGAGTACTCAAGAGCATCAGGGGATGGCTGGTAGCCTAGAAGGAACCACAAGGCCCAATGTCTTGGTTAGTCAAACCAATGAATTAGCTAGCAGGGGCCTTCTGAACAAAAGCAT
+
ADEEB@?CBBCCBDCBDCCCFBD;EEBEBBABCEC:EEBEAADCFCDFBFECCFCFFFFCCGFEDGFBBEEDCAECCEEBCECBDBCEEDCCBCBFAECCFEACAEAEBCCDCBCBFB:;CAEDCAEDBEEEEDC?<ECFBCDBCCCEDAA
#+begin_src
zgrep -A 3 "A00853:477:HMLWYDSX3:1:1413:4390:28573" /Work/Projects/bisonex/centogene/fastq/2200467051_63003856/63003856_S135_R1_001.fastq.gz
#+end_src
#+RESULTS:
: @A00853:477:HMLWYDSX3:1:1413:4390:28573 1:N:0:ATTCCACACA+TAGGCGATTG
AGGGTTACCACCACCACCCTGACAGGAGATATTCTAGGAGTACTCAAGAGCATCAGGGGATGGCTGGTAGCCTAGAAGGAACCACAAGGCCCAATGTCTTGGTTAGTCAAACCAATGAATTAGCTAGCAGGGGCCTTCTGAACAAAAGCAT
: +
: FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFF
******** DONE Regarder la qualité après bwa mem vs applybqsr: différente
CLOSED: [2023-05-24 Wed 22:18]
Sur le mésocentre, dans /Work/Users/apraga/bisonex/out/63003856_S135_R/preprocessing
$ samtools view mapped/63003856_S135_R.bam NC_000022.11 | rg "A00853:477:HMLWYDSX3:1:1413:4390:28573"
A00853:477:HMLWYDSX3:1:1413:4390:28573	163	NC_000022.11	42212845	0	151M	=	42212883	189	CCCAGGGGCCCCAGTGGGGATTTTCTAATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT	FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:151	MC:Z:151M	AS:i:151	XS:i:151	RG:Z:sample
A00853:477:HMLWYDSX3:1:1413:4390:28573	83	NC_000022.11	42212883	0	151M	=	42212845	-189	ATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACTCCTAGAATATCTCCTGTCAGGGTGGTGGTGGTAACCCT	FFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:151	MC:Z:151M	AS:i:151	XS:i:151	RG:Z:sample
samtools view applybqsr/63003856_S135_R.bam NC_000022.11 | rg "A00853:477:HMLWYDSX3:1:1413:4390:28573"
A00853:477:HMLWYDSX3:1:1413:4390:28573	163	NC_000022.11	42212845	0	151M	=	42212883	189	CCCAGGGGCCCCAGTGGGGATTTTCTAATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT	ACC+FBCDCBBBAEAEDEEBBCCCECACBAEBEBDCCBCBFDCCCCFACEBEBCEEDCCCCFDCAEDCACBCEBBCFEACCFBDCACDCBCEBDBBCFEEDCCCFAFEACECCCECAEEDCADCBEDC7BEBCCCFBAFDCECCFBEAACA	MC:Z:151M	MD:Z:151	PG:Z:MarkDuplicates	RG:Z:sample	NM:i:0	AS:i:151	XS:i:151
A00853:477:HMLWYDSX3:1:1413:4390:28573	83	NC_000022.11	42212883	0	151M	=	42212845	-189	ATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACTCCTAGAATATCTCCTGTCAGGGTGGTGGTGGTAACCCT	AADECCCBDCBFCE<?CDEEEEBDEACDEAC;:BFBCBCDCCBEAEACAEFCCEAFBCBCCDEECBDBCECBEECCEACDEEBBFGDEFGCCFFFFCFCCEFBFDCFCDAAEBEE:CECBABBEBEE;DBFCCCDBCDBCCBBC?@BEEDA	MC:Z:151M	MD:Z:151	PG:Z:MarkDuplicates	RG:Z:sample	NM:i:0	AS:i:151	XS:i:151
******** DONE Réaligner à partir de la sortie de bwa mem
CLOSED: [2023-05-24 Wed 22:32]
#+begin_src sh
cd out/63003856_S135_R/preprocessing/mapped/
samtools view 63003856_S135_R.bam NC_000022.11  -f 0x2 -o 63003856_chr22.bam
samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorted.bam
samtools fastq -1 63003856_chr22_1.fq.gz -2 63003856_chr22_2.fq.gz -0 /dev/null -s /dev/null -n 63003856_chr22_sorted.bam
#+end_src
ON vérifie la qualité
#+begin_src
zgrep -A 3 "A00853:477:HMLWYDSX3:1:1413:4390:28573" 63003856_chr22_1.fq.gz
#+end_src
#+RESULTS:
: @A00853:477:HMLWYDSX3:1:1413:4390:28573
: AGGGTTACCACCACCACCCTGACAGGAGATATTCTAGGAGTACTCAAGAGCATCAGGGGATGGCTGGTAGCCTAGAAGGAACCACAAGGCCCAATGTCTTGGTTAGTCAAACCAATGAATTAGCTAGCAGGGGCCTTCTGAACAAAAGCAT
: +
: FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFF
#+begin_src
NXF_OPTS=-D"user.name=apraga" nextflow run main.nf -c nextflow.config  -profile standard,helios -resume  --input="out/63003856_S135_R/preprocessing/mapped/63003856_chr22_{1,2}.fq.gz" --outdir=out/63003856_chr22-from-mapped
#+end_src
Puis ::
#+begin_src
cd /Work/Users/apraga/bisonex/out/63003856_chr22-from-mapped/63003856_chr22/preprocessing/mapped
samtools view 63003856_chr22.bam | rg "A00853:477:HMLWYDSX3:1:1413:4390:28573"
#+end_src
#+RESULTS:
: A00853:477:HMLWYDSX3:1:1413:4390:28573	163	NW_014040930.1	115017	0	151M	=	115055	189	CCCAGGGGCCCCAGTGGGGATTTTCTAATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT	FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:151	MC:Z:151M	AS:i:151	XS:i:151	RG:Z:sample
: A00853:477:HMLWYDSX3:1:1413:4390:28573	83	NW_014040930.1	115055	0	151M	=	115017	-189	ATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACTCCTAGAATATCTCCTGTCAGGGTGGTGGTGGTAACCCT	FFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:151	MC:Z:151M	AS:i:151	XS:i:151	RG:Z:sample
******* DONE Aligner sur génome de référence limité au chromosome 22
CLOSED: [2023-05-24 Wed 23:18]
******** KILL Test données non modifiées
CLOSED: [2023-05-24 Wed 23:18]
/Work/Users/apraga/bisonex/tests/bamscissors
#+begin_src
cd /Work/Groups/bisonex/data/genome/GRCh38.p13/
mkdir chr22/
samtools faidx genomeRef.fna NC_000022.11 > chr22/chr22.fna
cd chr22
samtools faidx chr22.fna
bwa index chr22.fna
#+end_src
#+begin_src
cd /Work/Users/apraga/bisonex/tests/bamscissors
ln -s ../../out/63003856_S135_R/preprocessing/applybqsr/63003856_chr22_{1,2}.fq.gz .
srun -c 24 -p smp -t 1:00:00 --pty bash
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/chr22/chr22.fna 63003856_chr22_1.fq.gz 63003856_chr22_1.fq.gz -o smallref.sam
#+end_src
******** DONE Test données modifiées: ok
CLOSED: [2023-05-24 Wed 23:18]
Données dans data/init
#+begin_src sh
time julia insertVariant.jl
rsync -avz data/init/*.fq.gz meso:/Work/Users/apraga/bisonex/tests/bamscissors/
#+end_src
#+begin_src
srun -c 24 -p smp -t 1:00:00 --pty bash
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/chr22/chr22.fna 63003856_chr22_1.fq.gz 63003856_chr22_1.fq.gz | samtools sort -@24 - -o smallref.bam
#+end_src
#+begin_src
rsync -avz meso:/Work/Users/apraga/bisonex/tests/bamscissors/smallref.bam mapped/
#+end_src
****** DONE Test haplotypecaller 1 variant
CLOSED: [2023-05-29 Mon 15:38]
****** DONE Test haplotypecaller tous les variants
***** TODO PHase 3 : tous les SNV
**** TODO Test Indel
*** Divers
**** DONE Vérifier nombre de reads fastq - bam
CLOSED: [2022-10-09 Sun 22:31]

[2.26896]

CDEECBDBCECBEECCEACDEEBBFGDEFGCCFFFFCFCCEFBFDCFCDAAEBEE:CECBABBEBEE;DBFCCCDBCDBCCBBC?@BEEDA	NM:i:0	MD:Z:151	MC:Z:151M	AS:i:151	XS:i:151	RG:Z:sample
Effectivement, on aligne sur une zonne supprimée !
******* DONE Corriger la qualité: non
CLOSED: [2023-05-24 Wed 22:19]
******** DONE Comparaison avec le fastq de référénce : qualité !!
CLOSED: [2023-05-24 Wed 22:17]
#+begin_src sh
cd /Work/Users/apraga/bisonex/work/6e/8548fc90263830bf677f36585f11dc
zgrep -A 3 "A00853:477:HMLWYDSX3:1:1413:4390:28573" 63003856_chr22_1.fq.gz
#+end_src
@A00853:477:HMLWYDSX3:1:1413:4390:28573
AGGGTTACCACCACCACCCTGACAGGAGATATTCTAGGAGTACTCAAGAGCATCAGGGGATGGCTGGTAGCCTAGAAGGAACCACAAGGCCCAATGTCTTGGTTAGTCAAACCAATGAATTAGCTAGCAGGGGCCTTCTGAACAAAAGCAT
+
ADEEB@?CBBCCBDCBDCCCFBD;EEBEBBABCEC:EEBEAADCFCDFBFECCFCFFFFCCGFEDGFBBEEDCAECCEEBCECBDBCEEDCCBCBFAECCFEACAEAEBCCDCBCBFB:;CAEDCAEDBEEEEDC?<ECFBCDBCCCEDAA
#+begin_src
zgrep -A 3 "A00853:477:HMLWYDSX3:1:1413:4390:28573" /Work/Projects/bisonex/centogene/fastq/2200467051_63003856/63003856_S135_R1_001.fastq.gz
#+end_src
#+RESULTS:
: @A00853:477:HMLWYDSX3:1:1413:4390:28573 1:N:0:ATTCCACACA+TAGGCGATTG
AGGGTTACCACCACCACCCTGACAGGAGATATTCTAGGAGTACTCAAGAGCATCAGGGGATGGCTGGTAGCCTAGAAGGAACCACAAGGCCCAATGTCTTGGTTAGTCAAACCAATGAATTAGCTAGCAGGGGCCTTCTGAACAAAAGCAT
: +
: FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFF
******** DONE Regarder la qualité après bwa mem vs applybqsr: différente
CLOSED: [2023-05-24 Wed 22:18]
Sur le mésocentre, dans /Work/Users/apraga/bisonex/out/63003856_S135_R/preprocessing
$ samtools view mapped/63003856_S135_R.bam NC_000022.11 | rg "A00853:477:HMLWYDSX3:1:1413:4390:28573"
A00853:477:HMLWYDSX3:1:1413:4390:28573	163	NC_000022.11	42212845	0	151M	=	42212883	189	CCCAGGGGCCCCAGTGGGGATTTTCTAATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT	FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:151	MC:Z:151M	AS:i:151	XS:i:151	RG:Z:sample
A00853:477:HMLWYDSX3:1:1413:4390:28573	83	NC_000022.11	42212883	0	151M	=	42212845	-189	ATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACTCCTAGAATATCTCCTGTCAGGGTGGTGGTGGTAACCCT	FFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:151	MC:Z:151M	AS:i:151	XS:i:151	RG:Z:sample
samtools view applybqsr/63003856_S135_R.bam NC_000022.11 | rg "A00853:477:HMLWYDSX3:1:1413:4390:28573"
A00853:477:HMLWYDSX3:1:1413:4390:28573	163	NC_000022.11	42212845	0	151M	=	42212883	189	CCCAGGGGCCCCAGTGGGGATTTTCTAATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT	ACC+FBCDCBBBAEAEDEEBBCCCECACBAEBEBDCCBCBFDCCCCFACEBEBCEEDCCCCFDCAEDCACBCEBBCFEACCFBDCACDCBCEBDBBCFEEDCCCFAFEACECCCECAEEDCADCBEDC7BEBCCCFBAFDCECCFBEAACA	MC:Z:151M	MD:Z:151	PG:Z:MarkDuplicates	RG:Z:sample	NM:i:0	AS:i:151	XS:i:151
A00853:477:HMLWYDSX3:1:1413:4390:28573	83	NC_000022.11	42212883	0	151M	=	42212845	-189	ATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACTCCTAGAATATCTCCTGTCAGGGTGGTGGTGGTAACCCT	AADECCCBDCBFCE<?CDEEEEBDEACDEAC;:BFBCBCDCCBEAEACAEFCCEAFBCBCCDEECBDBCECBEECCEACDEEBBFGDEFGCCFFFFCFCCEFBFDCFCDAAEBEE:CECBABBEBEE;DBFCCCDBCDBCCBBC?@BEEDA	MC:Z:151M	MD:Z:151	PG:Z:MarkDuplicates	RG:Z:sample	NM:i:0	AS:i:151	XS:i:151
******** DONE Réaligner à partir de la sortie de bwa mem
CLOSED: [2023-05-24 Wed 22:32]
#+begin_src sh
cd out/63003856_S135_R/preprocessing/mapped/
samtools view 63003856_S135_R.bam NC_000022.11  -f 0x2 -o 63003856_chr22.bam
samtools sort -n 63003856_chr22.bam -o 63003856_chr22_sorted.bam
samtools fastq -1 63003856_chr22_1.fq.gz -2 63003856_chr22_2.fq.gz -0 /dev/null -s /dev/null -n 63003856_chr22_sorted.bam
#+end_src
ON vérifie la qualité
#+begin_src
zgrep -A 3 "A00853:477:HMLWYDSX3:1:1413:4390:28573" 63003856_chr22_1.fq.gz
#+end_src
#+RESULTS:
: @A00853:477:HMLWYDSX3:1:1413:4390:28573
: AGGGTTACCACCACCACCCTGACAGGAGATATTCTAGGAGTACTCAAGAGCATCAGGGGATGGCTGGTAGCCTAGAAGGAACCACAAGGCCCAATGTCTTGGTTAGTCAAACCAATGAATTAGCTAGCAGGGGCCTTCTGAACAAAAGCAT
: +
: FFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFF
#+begin_src
NXF_OPTS=-D"user.name=apraga" nextflow run main.nf -c nextflow.config  -profile standard,helios -resume  --input="out/63003856_S135_R/preprocessing/mapped/63003856_chr22_{1,2}.fq.gz" --outdir=out/63003856_chr22-from-mapped
#+end_src
Puis ::
#+begin_src
cd /Work/Users/apraga/bisonex/out/63003856_chr22-from-mapped/63003856_chr22/preprocessing/mapped
samtools view 63003856_chr22.bam | rg "A00853:477:HMLWYDSX3:1:1413:4390:28573"
#+end_src
#+RESULTS:
: A00853:477:HMLWYDSX3:1:1413:4390:28573	163	NW_014040930.1	115017	0	151M	=	115055	189	CCCAGGGGCCCCAGTGGGGATTTTCTAATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT	FFF,FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:151	MC:Z:151M	AS:i:151	XS:i:151	RG:Z:sample
: A00853:477:HMLWYDSX3:1:1413:4390:28573	83	NW_014040930.1	115055	0	151M	=	115017	-189	ATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACTCCTAGAATATCTCCTGTCAGGGTGGTGGTGGTAACCCT	FFFFFFFFFFFFFF::FFFFFFFFFFFFFFF::FFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFFF:FFFFFFFFFFF:FFFFFFFFFFFFFFFFFFFFFFF	NM:i:0	MD:Z:151	MC:Z:151M	AS:i:151	XS:i:151	RG:Z:sample
******* DONE Aligner sur génome de référence limité au chromosome 22
CLOSED: [2023-05-24 Wed 23:18]
******** KILL Test données non modifiées
CLOSED: [2023-05-24 Wed 23:18]
/Work/Users/apraga/bisonex/tests/bamscissors
#+begin_src
cd /Work/Groups/bisonex/data/genome/GRCh38.p13/
mkdir chr22/
samtools faidx genomeRef.fna NC_000022.11 > chr22/chr22.fna
cd chr22
samtools faidx chr22.fna
bwa index chr22.fna
#+end_src
#+begin_src
cd /Work/Users/apraga/bisonex/tests/bamscissors
ln -s ../../out/63003856_S135_R/preprocessing/applybqsr/63003856_chr22_{1,2}.fq.gz .
srun -c 24 -p smp -t 1:00:00 --pty bash
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/chr22/chr22.fna 63003856_chr22_1.fq.gz 63003856_chr22_1.fq.gz -o smallref.sam
#+end_src
******** DONE Test données modifiées: ok
CLOSED: [2023-05-24 Wed 23:18]
Données dans data/init
#+begin_src sh
time julia insertVariant.jl
rsync -avz data/init/*.fq.gz meso:/Work/Users/apraga/bisonex/tests/bamscissors/
#+end_src
#+begin_src
srun -c 24 -p smp -t 1:00:00 --pty bash
bwa mem -t 24 /Work/Projects/bisonex/data/genome/GRCh38.p13/chr22/chr22.fna 63003856_chr22_1.fq.gz 63003856_chr22_1.fq.gz | samtools sort -@24 - -o smallref.bam
#+end_src
#+begin_src
rsync -avz meso:/Work/Users/apraga/bisonex/tests/bamscissors/smallref.bam mapped/
#+end_src
****** DONE Test haplotypecaller 1 variant
CLOSED: [2023-05-29 Mon 15:38]
****** DONE Test haplotypecaller tous les variants
****** TODO Comprendre pourquoi la répartiton ne suit pas la loi normale
Certains hétérozygote soint à 0.01 ou 1...
******* DONE augmenter le nombre d'échantillions: idem
CLOSED: [2023-05-31 Wed 22:24]
******* TODO Vérifier le nombre de reads marqué vs édité
******* DONE vérifier que 100 appel à rand(d, 1)[1] est semblable à un appel de rand(d, 100)
CLOSED: [2023-05-31 Wed 22:24]
julia> df = vcat(DataFrame(:y => z, :type => "z"), DataFrame(:y => y, :type => "y"));
julia> y = [rand(d, 1)[1] for x in 1:1000];
julia> z = rand(d,1000);
julia> df = vcat(DataFrame(:y => z, :type => "z"), DataFrame(:y => y, :type => "y"));
 draw(data(df)*histogram(bins=100)*mapping(:y, color=:type,dodge=:type))
****** TODO Refaire le test avec la nouvelle version
Mésocentre
#+begin_src sh
cd /Work/Users/apraga/bisonex/out/63003856_S135_R/preprocessing/mapped
samtools view 63003856_S135_R.bam NC_000022.11 -o 63003856_S135_R_chr22.bam
#+end_src
Génération locale du fichier
#+begin_src sh :dir /home/alex/roam/recherche/bisonex/code/xamscissors
~/.local/julia-1.9.0/bin/julia --project=.. snvs.jl
rsync -avz meso:/Work/Users/apraga/bisonex/out/63003856_S135_R/preprocessing/mapped/63003856_S135_R_chr22.bam .
samtools index 63003856_S135_R_chr22.bam
#+end_src
#+RESULTS:
| receiving | incremental | file  | list        |         |       |              |           |
|           |             |       |             |         |       |              |           |
| sent      | 20          | bytes | received    |      79 | bytes |         66.0 | bytes/sec |
| total     | size        | is    | 143,162,969 | speedup | is    | 1,446,090.60 |           |
On génère les données
#+begin_src julia
using XAMScissors
insertSNV("./63003856_S135_R_chr22.bam", "snvs_chr22.csv", "out")
#+end_src
Puis
#+begin_src sh
~/.local/julia-1.9.0/bin/julia --project=.. xamscissors.jl
#+end_src
***** TODO PHase 3 : tous les SNV
**** TODO Test Indel
*** Divers
**** DONE Vérifier nombre de reads fastq - bam
CLOSED: [2022-10-09 Sun 22:31]

File addition: 20230531095805-julia.org (----------)

[4.29]

:PROPERTIES:
:ID:       606cfb9e-0210-46eb-abcb-c03ef5522464
:END:
#+title: Julia
#+filetags: personal julia
* Tester un paquet localement
#+begin_src
$ julia
julia> ]
(@v1.9) pkg> develop /home/alex/code/XAMScissors.jl
#+end_src
Puis il suffit d'utiliser le paquet. En cas de changement, la precompilation sera refait à chaque fois
#+begin_src
julia> using XAMScissors
#+end_src