 Thomas
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63632f0b37
keep ancient mtime when modifying BAM header for adding SM tag in Mutect2
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il y a 3 semaines |
|
Thomas
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0ee77e1f7c
adding SM tag on BAM header during impory
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il y a 3 semaines |
|
Thomas
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83f7501240
bug: GATK mutect2 use SM tag but no tag if no barcode by dorado. solution: add sm tag and reheader
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il y a 3 semaines |
|
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/
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il y a 3 semaines |
|
Thomas
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069f6f8b38
Added GATK mutect2
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il y a 3 semaines |
|
Thomas
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73775d23a0
clean
|
il y a 1 mois |
|
Thomas
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94e3fdb614
clean
|
il y a 1 mois |
|
Thomas
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5133ac3efd
liftover
|
il y a 1 mois |
|
Thomas
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6422cbd96f
m
|
il y a 1 mois |
|
Thomas
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e5838fa74e
lim s batch para
|
il y a 1 mois |
|
Thomas
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48a6cb89db
upated straglr job_name to refelct the sample and part
|
il y a 1 mois |
|
Thomas
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aad235db3d
upated straglr job_name to refelct the sample and part
|
il y a 1 mois |
|
Thomas
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354d5c9a42
upated straglr job_name to refelct the sample and part
|
il y a 1 mois |
|
Thomas
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fc28b7c1a7
m
|
il y a 1 mois |
|
Thomas
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1ce719023c
better concurrency in job execution
|
il y a 1 mois |
|
Thomas
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6a81179dfb
added SomaticScan in callers pipe
|
il y a 1 mois |
|
Thomas
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538e30df2e
added should_run for LongphaseHap run
|
il y a 1 mois |
|
Thomas
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72159af3ec
bug HP bam double suffixe
|
il y a 1 mois |
|
Thomas
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66faf6060c
upgraded jobs names with part index
|
il y a 1 mois |
|
Thomas
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95062589e6
limit clairs mem
|
il y a 1 mois |
|
Thomas
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d17bbe3ad5
limit clairs threads
|
il y a 1 mois |
|
Thomas
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a6e037983f
limit max sbatch in paral for run_many_sbatch
|
il y a 1 mois |
|
Thomas
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93f5594588
rm lock in chunked run fn
|
il y a 1 mois |
|
Thomas
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85fae9dc92
should_run befor lock
|
il y a 1 mois |
|
Thomas
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30c12c86c4
Repat annoation
|
il y a 1 mois |
|
Thomas
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c2301c5f98
one source of hash
|
il y a 1 mois |
|
Thomas
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478f26daf0
improved BAM INS detection
|
il y a 1 mois |
|
Thomas
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0278ed4c64
improved somatic pipe
|
il y a 2 mois |
|
Thomas
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91263c0e19
somatic_depth_quality_ranges bug fix
|
il y a 2 mois |
|
Thomas
|
f6064be4ee
somatic_depth_quality_ranges bug fix
|
il y a 2 mois |
