 Thomas
|
dce4a111cc
nanomonsv -> mediumq; GATK ok
|
hai 5 días |
|
Thomas
|
9ddb488f87
robuster epilog parsing
|
hai 6 días |
|
Thomas
|
22d9b9f29d
savana_mem for slurm max mem
|
hai 6 días |
|
Thomas
|
f216c34dce
reduced clairS threads; added slurm_max_par default: 10; use of run! and run_many! in bam import
|
hai 1 semana |
|
Thomas
|
27489a85bc
config;panel_bam
|
hai 1 semana |
|
Thomas
|
a631c652db
Infos.freq_maf()
|
hai 2 semanas |
|
Thomas
|
9e3c086a44
Infos fields for dbSNP
|
hai 2 semanas |
|
Thomas
|
fe19eb6036
scan remove chrM
|
hai 1 mes |
|
Thomas
|
caee96be9e
scan remove chrM
|
hai 1 mes |
|
Thomas
|
96474698f0
scan remove chrM
|
hai 1 mes |
|
Thomas
|
841fa84fa2
unactivate reheader
|
hai 1 mes |
|
Thomas
|
947fe471aa
save_into_lifted for Variants
|
hai 2 meses |
|
Thomas
|
fd1dc2c8df
sm tags modif
|
hai 2 meses |
|
Thomas
|
63632f0b37
keep ancient mtime when modifying BAM header for adding SM tag in Mutect2
|
hai 2 meses |
|
Thomas
|
0ee77e1f7c
adding SM tag on BAM header during impory
|
hai 2 meses |
|
Thomas
|
83f7501240
bug: GATK mutect2 use SM tag but no tag if no barcode by dorado. solution: add sm tag and reheader
|
hai 2 meses |
|
Thomas
|
4690b66eea
bug: GATK mutect2 SM tag in normal bam not corresponding to sample_name in CMD line. solution: parse SM tag and use it as sample_name. caveat: no verification vbut as long names are generic and attributed by ssystem ok/
|
hai 2 meses |
|
Thomas
|
069f6f8b38
Added GATK mutect2
|
hai 2 meses |
|
Thomas
|
73775d23a0
clean
|
hai 2 meses |
|
Thomas
|
94e3fdb614
clean
|
hai 2 meses |
|
Thomas
|
5133ac3efd
liftover
|
hai 2 meses |
|
Thomas
|
6422cbd96f
m
|
hai 3 meses |
|
Thomas
|
e5838fa74e
lim s batch para
|
hai 3 meses |
|
Thomas
|
48a6cb89db
upated straglr job_name to refelct the sample and part
|
hai 3 meses |
|
Thomas
|
aad235db3d
upated straglr job_name to refelct the sample and part
|
hai 3 meses |
|
Thomas
|
354d5c9a42
upated straglr job_name to refelct the sample and part
|
hai 3 meses |
|
Thomas
|
fc28b7c1a7
m
|
hai 3 meses |
|
Thomas
|
1ce719023c
better concurrency in job execution
|
hai 3 meses |
|
Thomas
|
6a81179dfb
added SomaticScan in callers pipe
|
hai 3 meses |
|
Thomas
|
538e30df2e
added should_run for LongphaseHap run
|
hai 3 meses |
