- [[Centogene config]]
-

- On vérifie après alignement : 19 de profondeur (attention il faut -Q 0 pour correspondre)
- ```bash
  cd /Work/Users/apraga/bisonex/out/preprocessing/mapped/2200519525-63060439-GRCh38
  samtools mpileup 2200519525-63060439-GRCh38.aligned.bam -r chr15:26869324-26869324 -Q 0

- On vérifie que cela ne vient pas de l'alignement : GRCH38-noalt et GRCh37
- ```bash 

  [mpileup] 1 samples in 1 input files
  chr15   26869324        N       19      AaAaaTTATtTTttAattA     k:!k!!kFk!!kk!k!k!F
  ```
- On essaie avec la version noalt : idem !
- ```bash
  cd /Work/Users/apraga/bisonex/work/2c/63779dffb657b13fcfd2f4f09da8e2
  mv bwa .bwa
  ln -s /Work/Projects/bisonex/data/fasta/GRCh38-noalt/bwa .
  mv 2200519525-63060439-GRCh38.aligned.bam  2200519525-63060439-GRCh38.aligned-grch38.bam
  bwa mem     -R '@RG\tID:sample\tSM:sample\tPL:ILLUMINA\tPM:Miseq\tCN:CHU_Minjoz\tLB:definition_to_add'     -t 24     bwa/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna     63060439_S92_R1_001.fastq.gz 63060439_S92_R2_001.fastq.gz     | samtools sort  --threads 24 -o 2200519525-63060439-GRCh38.aligned.bam -
  samtools mpileup 2200519525-63060439-GRCh38.aligned.bam -r chr15:26869324-26869324 -Q 0

  bwa mem -R '@RG\tID:sample\tSM:sample\tPL:ILLUMINA\tPM:Miseq\tCN:CHU_Minjoz\tLB:definition_to_add'     -t 24   /Work/Groups/bisonex/data/fasta/GRCh37/hg19.p13.plusMT.no_alt_analysis_set/hg19.p13.plusMT.no_alt_analysis_set.fa     63060439_S92_R1_001.fastq.gz 63060439_S92_R2_001.fastq.gz     | samtools sort  --threads 24 -o 2200519525-63060439-GRCh37.aligned.bam -
  bwa mem -R '@RG\tID:sample\tSM:sample\tPL:ILLUMINA\tPM:Miseq\tCN:CHU_Minjoz\tLB:definition_to_add'     -t 24     /Work/Groups/bisonex/data/fasta/GRCh38-noalt/bwa/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna     63060439_S92_R1_001.fastq.gz 63060439_S92_R2_001.fastq.gz     | samtools sort  --threads 24 -o 2200519525-63060439-GRCh38-noalt.aligned.bam -
  

  samtools index 2200519525-63060439-GRCh37.aligned.bam
  samtools index 2200519525-63060439-GRCh38-noalt.aligned.bam
  samtools mpileup 2200519525-63060439-GRCh38-noalt.aligned.bam -r chr15:26869324-26869324 -Q 0

  ```
- Dernier test : avec GRCh37 no alt. Il n'y a pas la version avec les index bwa sur le FTP ncbi donc on utilise
- ```bash
  cd /Work/Groups/bisonex/data/fasta/GRCh37/
  wget https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/analysisSet/hg19.p13.plusMT.no_alt_analysis_set.fa.gz_pipelines/GCA_000001405.14_GRCh37.p13_no_alt_analysis_set.fna.g
  wget https://hgdownload.soe.ucsc.edu/goldenPath/hg19/bigZips/analysisSet/hg19.p13.plusMT.no_alt_analysis_set.bwa_index.tar.gz
  
  z bisonex
  cd test/gabra5
  ln -s /Work/Groups/bisonex/data/fasta/GRCh37/hg19.p13.plusMT.no_alt_analysis_set .
  bwa mem     -R '@RG\tID:sample\tSM:sample\tPL:ILLUMINA\tPM:Miseq\tCN:CHU_Minjoz\tLB:definition_to_add'     -t 24     hg19.p13.plusMT.no_alt_analysis_set/hg19.p13.plusMT.no_alt_analysis_set.fa     63060439_S92_R1_001.fastq.gz 63060439_S92_R2_001.fastq.gz     | samtools sort  --threads 24 -o 2200519525-63060439-GRCh37.aligned.bam -
  ```
- Après liftover (27114471), pareils ... 
  ```bash
   samtools mpileup 2200519525-63060439-GRCh37.aligned.bam -r chr15:27114471-27114471 -Q 0

  samtools mpileup 2200519525-63060439-GRCh37.aligned.bam -r chr15:27114471-27114471 -Q 0

- TODO: markduplicates
- gatk MarkDuplicates --INPUT 2200519525-63060439-GRCh37.aligned.bam --OUTPUT 2200519525-63060439-GRCh37.markedup.bam --REFERENCE_SEQUENCE /Work/Groups/bisonex/data/fasta/GRCh37/hg19.p13.plusMT.no_alt_analysis_set.fa.gz  --METRICS_FILE metrics
-
- TODO: tested freebays (cf VCF cento)

- Probablement un problème des fastq ? Argument en faveurs
	- pas eu ce problème sur les autres variants
	- bwa-mem semble signaler une erreur 
	  ```bash
	  [M::mem_process_seqs] Processed 734826 reads in 150.735 CPU sec, 6.449 real sec
	  [W::bseq_read] the 1st file has fewer sequences.
	  [W::bseq_read] the 1st file has fewer sequences.
	  [gzclose] buffer error
	  [bam_sort_core] merg
	  ```
- Effectivement : 
  ```bash
   du -hs *63060439*/*
  558M    2200519525_63060439/63060439_S92_R1_001.fastq.gz
  2.6G    2200519525_63060439/63060439_S92_R2_001.fastq.gz
  ```

- D'après un VCF
- Aligneur : freebayes
- Génome GRCh37p13

- GABRA5 : problème du fastq [[Comparaison à centogène]].
- Cento utilise freebayes d'après les VCF [[Centogene config]]