 Thomas
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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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hai 3 semanas |
|
Thomas
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069f6f8b38
Added GATK mutect2
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hai 3 semanas |
|
Thomas
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73775d23a0
clean
|
hai 1 mes |
|
Thomas
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94e3fdb614
clean
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hai 1 mes |
|
Thomas
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5133ac3efd
liftover
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hai 1 mes |
|
Thomas
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6422cbd96f
m
|
hai 1 mes |
|
Thomas
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e5838fa74e
lim s batch para
|
hai 1 mes |
|
Thomas
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48a6cb89db
upated straglr job_name to refelct the sample and part
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hai 1 mes |
|
Thomas
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aad235db3d
upated straglr job_name to refelct the sample and part
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hai 1 mes |
|
Thomas
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354d5c9a42
upated straglr job_name to refelct the sample and part
|
hai 1 mes |
|
Thomas
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fc28b7c1a7
m
|
hai 1 mes |
|
Thomas
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1ce719023c
better concurrency in job execution
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hai 1 mes |
|
Thomas
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6a81179dfb
added SomaticScan in callers pipe
|
hai 1 mes |
|
Thomas
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538e30df2e
added should_run for LongphaseHap run
|
hai 1 mes |
|
Thomas
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72159af3ec
bug HP bam double suffixe
|
hai 1 mes |
|
Thomas
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66faf6060c
upgraded jobs names with part index
|
hai 1 mes |
|
Thomas
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95062589e6
limit clairs mem
|
hai 1 mes |
|
Thomas
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d17bbe3ad5
limit clairs threads
|
hai 1 mes |
|
Thomas
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a6e037983f
limit max sbatch in paral for run_many_sbatch
|
hai 1 mes |
|
Thomas
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93f5594588
rm lock in chunked run fn
|
hai 1 mes |
|
Thomas
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85fae9dc92
should_run befor lock
|
hai 1 mes |
|
Thomas
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30c12c86c4
Repat annoation
|
hai 1 mes |
|
Thomas
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c2301c5f98
one source of hash
|
hai 1 mes |
|
Thomas
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478f26daf0
improved BAM INS detection
|
hai 1 mes |
|
Thomas
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0278ed4c64
improved somatic pipe
|
hai 2 meses |
|
Thomas
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91263c0e19
somatic_depth_quality_ranges bug fix
|
hai 2 meses |
|
Thomas
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f6064be4ee
somatic_depth_quality_ranges bug fix
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hai 2 meses |
|
Thomas
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fc120e0876
GenesBedIndex comment + rm sort dedup
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hai 2 meses |
|
Thomas
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ff594b7c02
GenesBedIndex
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hai 2 meses |
|
Thomas
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035d9d3741
config: added IGV and viz required files
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hai 2 meses |
