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config.yaml
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config.yaml
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---
ABL1:
ref: "chr9"
start: 130714369
end: 130854114
cigar_in: "M1396[0-1][1-9]N"
catg: "expr"
WT1:
ref: "chr11"
start: 32428042
end: 32434722
cigar_in: "M438N"
catg: "expr"
PRAME:
ref: "chr22"
start: 22548424
end: 22548559
seq_in: "^CGT"
catg: "expr"
NPM1_wt:
ref: "chr5"
start: 171407744
end: 171410635
cigar_out: "4I"
catg: "expr"
cigar_in: "[0-9]M2752N[0-9][0-9]M"
pos: 1714077
NPM1_mutant:
ref: "chr5"
start: 171407744
end: 171410635
cigar_in: "[0-9]M2752N[0-9][0-9]M4I"
catg: "expr"
PML-RARA_bcr1:
ref1: "chr17"
pos1: 40348315
ref2: "chr15"
pos2: 74033415
catg: "fusion"
r1:
ref: "chr17"
start: 40348316
end: 40348396
r2:
ref: "chr15"
start: 74033319
end: 74033414
PML-RARA_bcr3:
ref1: "chr17"
pos1: 40348315
ref2: "chr15"
pos2: 74023409
catg: "fusion"
r1:
ref: "chr17"
start: 40348316
end: 40348396
r2:
ref: "chr15"
start: 74023343
end: 74023408
RUNX1-RUNX1T1:
ref1: "chr8"
pos1: 92017364
ref2: "chr21"
pos2: 34859473
catg: "fusion"
r1:
ref: "chr21"
start: 34859474
end: 34859556
r2:
ref: "chr8"
start: 92017298
end: 92017363
BCR-ABL1_p190:
ref1: "chr9"
pos1: 130854063
ref2: "chr22"
pos2: 23182240
catg: "fusion"
r1:
ref: "chr22"
start: 23182069
end: 23182239
r2:
ref: "chr9"
start: 130854064
end: 130854114
BCR-ABL1_p210:
ref1: "chr9"
pos1: 130854063
ref2: "chr22"
pos2: 23290414
catg: "fusion"
r1:
ref: "chr22"
start: 23289558
end: 23290413
r2:
ref: "chr9"
start: 130854064
end: 130854114
CBFB-MYH11:
ref1: "chr16"
pos1: 15721052
ref2: "chr16"
pos2: 67082309
catg: "fusion"
r1:
ref: "chr16"
start: 67066750
end: 67082308
r2:
ref: "chr16"
start: 15720994
end: 15721051
CBFB-MYH11-rare:
ref: "chr16"
start: 15720994
end: 15721051
catg: "expr"
seq: "TCTTCATCTCCTCCATCTGGGTCTCCAGGGCCCGCTTGGACTTCTCCAGCTCATGGAC"
scriptPath: #path to scripts folder
StarIndex: #path to star Index
jobs_out: "out"
list_of_genes: ['ABL1','WT1','PRAME','NPM1_wt','NPM1_mutant']
list_of_fusions: ['CBFB-MYH11','RUNX1-RUNX1T1','PML-RARA_bcr1','BCR-ABL1_p190','BCR-ABL1_p210']