AATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT	ACC+FBCDCBBBAEAEDEEBBCCCECACBAEBEBDCCBCBFDCCCCFACEBEBCEEDCCCCFDCAEDCACBCEBBCFEACCFBDCACDCBCEBDBBCFEEDCCCFAFEACECCCECAEEDCADCBEDC7BEBCCCFBAFDCECCFBEAACA	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	AADECCCBDCBFCE<?CDEEEEBDEACDEAC;:BFBCBCDCCBEAEACAEFCCEAFBCBCCDEECBDBCECBEECCEACDEEBBFGDEFGCCFFFFCFCCEFBFDCFCDAAEBEE: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
**** TODO Phase 3 : insertion SNV chromosome 22 sur BAM complet + test haplotypecaller
*** Divers
**** DONE Vérifier nombre de reads fastq - bam
CLOSED: [2022-10-09 Sun 22:31]

AATAGAGACCCAATGCTTTTGTTCAGAAGGCCCCTGCTAGCTAATTCATTGGTTTGACTAACCAAGACATTGGGCCTTGTGGTTCCTTCTAGGCTACCAGCCATCCCCTGATGCTCTTGAGTACT	ACC+FBCDCBBBAEAEDEEBBCCCECACBAEBEBDCCBCBFDCCCCFACEBEBCEEDCCCCFDCAEDCACBCEBBCFEACCFBDCACDCBCEBDBBCFEEDCCCFAFEACECCCECAEEDCADCBEDC7BEBCCCFBAFDCECCFBEAACA	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	AADECCCBDCBFCE<?CDEEEEBDEACDEAC;:BFBCBCDCCBEAEACAEFCCEAFBCBCCDEECBDBCECBEECCEACDEEBBFGDEFGCCFFFFCFCCEFBFDCFCDAAEBEE: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
**** TODO Phase 3 : insertion SNV chromosome 22 sur BAM complet + test haplotypecaller
NXF_OPTS=-D"user.name=${USER}" nextflow run workflows/runInserted.nf -profile standard,helios  --input="tests/bamscissors/63003856_chr22_{1,2}.fq.gz" -resume
On vérifie le nombre de reads :
cd work/13/3faf1c868bfe61d22da346319b27aa/
samtools mpileup 63003856_chr22.bam -r NC_000022.11:42213078-42213078
[mpileup] 1 samples in 1 input files
NC_000022.11	42213078	N	18	GgGGgGGGgGGgGgGggg	bbZbbbbCbCC\Aa@bTb
rsync -avz meso:/Work/Users/apraga/bisonex/work/8d/b76d9079cc59a5daaefa74653d2a9d/63003856_chr22.bam\* mapped
ok
Après haplotypecaller
 rsync -avz meso:/Work/Users/apraga/bisonex/work/68/e50b99ecc879039086c4c1fc2f24d3/63003856_chr22.vcf.gz\* variantCalling
 On retrouve bien le variant !
*** Divers
**** DONE Vérifier nombre de reads fastq - bam
CLOSED: [2022-10-09 Sun 22:31]