 Thomas
|
0ee77e1f7c
adding SM tag on BAM header during impory
|
hace 3 semanas |
|
Thomas
|
83f7501240
bug: GATK mutect2 use SM tag but no tag if no barcode by dorado. solution: add sm tag and reheader
|
hace 3 semanas |
|
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/
|
hace 3 semanas |
|
Thomas
|
069f6f8b38
Added GATK mutect2
|
hace 3 semanas |
|
Thomas
|
73775d23a0
clean
|
hace 1 mes |
|
Thomas
|
94e3fdb614
clean
|
hace 1 mes |
|
Thomas
|
5133ac3efd
liftover
|
hace 1 mes |
|
Thomas
|
6422cbd96f
m
|
hace 1 mes |
|
Thomas
|
e5838fa74e
lim s batch para
|
hace 1 mes |
|
Thomas
|
48a6cb89db
upated straglr job_name to refelct the sample and part
|
hace 1 mes |
|
Thomas
|
aad235db3d
upated straglr job_name to refelct the sample and part
|
hace 1 mes |
|
Thomas
|
354d5c9a42
upated straglr job_name to refelct the sample and part
|
hace 1 mes |
|
Thomas
|
fc28b7c1a7
m
|
hace 1 mes |
|
Thomas
|
1ce719023c
better concurrency in job execution
|
hace 1 mes |
|
Thomas
|
6a81179dfb
added SomaticScan in callers pipe
|
hace 1 mes |
|
Thomas
|
538e30df2e
added should_run for LongphaseHap run
|
hace 1 mes |
|
Thomas
|
72159af3ec
bug HP bam double suffixe
|
hace 1 mes |
|
Thomas
|
66faf6060c
upgraded jobs names with part index
|
hace 1 mes |
|
Thomas
|
95062589e6
limit clairs mem
|
hace 1 mes |
|
Thomas
|
d17bbe3ad5
limit clairs threads
|
hace 1 mes |
|
Thomas
|
a6e037983f
limit max sbatch in paral for run_many_sbatch
|
hace 1 mes |
|
Thomas
|
93f5594588
rm lock in chunked run fn
|
hace 1 mes |
|
Thomas
|
85fae9dc92
should_run befor lock
|
hace 1 mes |
|
Thomas
|
30c12c86c4
Repat annoation
|
hace 1 mes |
|
Thomas
|
c2301c5f98
one source of hash
|
hace 1 mes |
|
Thomas
|
478f26daf0
improved BAM INS detection
|
hace 1 mes |
|
Thomas
|
0278ed4c64
improved somatic pipe
|
hace 2 meses |
|
Thomas
|
91263c0e19
somatic_depth_quality_ranges bug fix
|
hace 2 meses |
|
Thomas
|
f6064be4ee
somatic_depth_quality_ranges bug fix
|
hace 2 meses |
|
Thomas
|
fc120e0876
GenesBedIndex comment + rm sort dedup
|
hace 2 meses |
