**** TODO Alignement
***** DONE Brut
CLOSED: [2022-12-26 Mon 22:03]
Bam alexis
$ samtools view -c /Work/Groups/bisonex/ref_63003856_S135/63003856_S135.bam
128077207
Notre
9f/26cf3d] Cached process > preprocess:BWA_MEM (63003856_S135)
$ samtools view -c work/9f/26cf3deb07b425a3e851be2a7bd782/63003856_S135.bam
On vérifie la sortie
$ samtools view -c out/63003856_S135/preprocessing/mapped/63003856_S135.bam
128077211
Petite différence (< 1e-8) mais selon Alexis, bwa mem est non reproductible. d'autant qu'on utilise une version parallélisée
128077211
On vérifie les arguments: ok
***** DONE Nettoyé
CLOSED: [2022-12-26 Mon 22:08]
On regarde les stats en détails (de la version nettoyée)
[57/4b5b4c] Cached process > preprocess:GATK4_CLEANSAM (63003856_S135)
$ samtools view -c work/57/4b5b4c647b98bb7099c4d1ba24bd75/63003856_S135.bam
128077211
Et la sortie
$ samtools view -c out/63003856_S135/preprocessing/clean-sam/sorted.bam
128077211
$ samtools flagstat work/57/4b5b4c647b98bb7099c4d1ba24bd75/63003856_S135.bam
128077211 + 0 in total (QC-passed reads + QC-failed reads)
126905130 + 0 primary
0 + 0 secondary
1172081 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
127941054 + 0 mapped (99.89% : N/A)
126768973 + 0 primary mapped (99.89% : N/A)
126905130 + 0 paired in sequencing
63452565 + 0 read1
63452565 + 0 read2
125263664 + 0 properly paired (98.71% : N/A)
126676024 + 0 with itself and mate mapped
92949 + 0 singletons (0.07% : N/A)
979608 + 0 with mate mapped to a different chr
675398 + 0 with mate mapped to a different chr (mapQ>=5)
$ samtools flagstat /Work/Groups/bisonex/ref_63003856_S135/63003856_S135_cleaned.bam
128077207 + 0 in total (QC-passed reads + QC-failed reads)
126905130 + 0 primary
0 + 0 secondary
1172077 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
127941051 + 0 mapped (99.89% : N/A)
126768974 + 0 primary mapped (99.89% : N/A)
126905130 + 0 paired in sequencing
63452565 + 0 read1
63452565 + 0 read2
125263790 + 0 properly paired (98.71% : N/A)
126676026 + 0 with itself and mate mapped
92948 + 0 singletons (0.07% : N/A)
979618 + 0 with mate mapped to a different chr
675412 + 0 with mate mapped to a different chr (mapQ>=5)