apraga/org - Change ZZPVFXEHFL3QNDP4AMCX5OFVDJUO6NR5MNYH2EUW2DL2R3OG6SIQC

Bisonex

Created by Alexis Praga on February 22, 2023

ZZPVFXEHFL3QNDP4AMCX5OFVDJUO6NR5MNYH2EUW2DL2R3OG6SIQC

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Change contents

Insertion in projects/bisonex.org at line 2992 [3.35]

[2.1449]

On récupére 2 échantillons pour ce patient sur HiSeq Exome
#+begin_src sh :dir /ssh:meso:/Work/Groups/bisonex/data/giab/GRCh38
wget https://raw.githubusercontent.com/genome-in-a-bottle/giab_data_indexes/master/NA12878/alignment.index.NA12878_HiSeq_Exome_Garvan_GRCh37_09252015 -O todl.txt
awk '{print $1}' todl.txt | wget -i -
#+end_src
On récupére le premier échantillons en prenant just le chromosome 1

Replacement in projects/bisonex.org at line 2999 [3.35]

B:BD[2.1461] → [2.1461:2244]

wget
ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/OsloUniversityHospital_Exome/151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008.posiSrt.markDup.bam
wget ftp://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/OsloUniversityHospital_Exome/151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008.posiSrt.markDup.bai
mv 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008.posiSrt.markDup.bam NA12878_illumina_exome.bam
mv 151002_7001448_0359_AC7F6GANXX_Sample_HG002-EEogPU_v02-KIT-Av5_AGATGTAC_L008.posiSrt.markDup.bai NA12878_illumina_exome.bai
 samtools view -b NA12878_illumina_exome.bam 1 > NA12878_illumina_exome_chr1.bam

[2.1461]

[2.2244]

samtools merge NA12878-NIST7035-HiSeq_Exome_Garan_GRCh37.bam project
.NIST_NIST7035_H7AP8ADXX_TAAGGCGA_1_NA12878.bwa.markDuplicates.bam project.NIST_NIST7035_H7AP8ADXX_TA
AGGCGA_2_NA12878.bwa.markDuplicates.bam
samtools index NA12878-NIST7035-HiSeq_Exome_Garan_GRCh37.bam

Replacement in projects/bisonex.org at line 3004 [3.35]

B:BD[2.2254] → [2.2254:2275]

On va couper le chr1

[2.2254]

[4.818]

***** TODO Filtrer variants introniques de référence avec vep
****** TODO variant calling seulf + seulement -f: nombreux FP
/Work/Users/apraga/bisonex/work/68/f1cf72a5a4078fdf743fb3844b369a
 Type Filter  TRUTH.TOTAL  TRUTH.TP  TRUTH.FN  QUERY.TOTAL  QUERY.FP  QUERY.UNK  FP.gt  FP.al  METRIC.Recall  METRIC.Precision
INDEL    ALL          519       284       235        52169     37789      14094     12     64       0.547206          0.007511
INDEL   PASS          519       284       235        52169     37789      14094     12     64       0.547206          0.007511
  SNP    ALL        22131     17434      4697       357652    305313      34904    189     32       0.787764          0.054020
  SNP   PASS        22131     17434      4697       357652    305313      34904    189     32       0.787764          0.054020
 METRIC.Frac_NA  METRIC.F1_Score  TRUTH.TOTAL.TiTv_ratio  QUERY.TOTAL.TiTv_ratio  TRUTH.TOTAL.het_hom_ratio  QUERY.TOTAL.het_hom_ratio
       0.270160         0.014820                     NaN                     NaN                   1.775956                   0.509510
       0.270160         0.014820                     NaN                     NaN                   1.775956                   0.509510
       0.097592         0.101108                2.971834                1.429533                   1.579776                   0.324923
       0.097592         0.101108                2.971834                1.429533                   1.579776                   0.324923