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I have this region, which seems to be LOH based on GATK-CNV and titan call, however, upon correction it becomes NEUT (chr2:196889180;242814009). Guess I am missing something, but correction would adjust for purity and impact HLAMP regions etc, correct?
Chromosome
Start_Position.bp.
End_Position.bp.
Length.snp.
Median_Ratio
Median_logR
TITAN_state
TITAN_call
Copy_Number
MinorCN
MajorCN
Clonal_Cluster
Cellular_Prevalence
logR_Copy_Number
Corrected_Ratio
Corrected_Copy_Number
Corrected_Call
Corrected_MajorCN
Corrected_MinorCN
2
672745
79314081
529
0.59
0.15
5
GAIN
3
1
2
1
1
2.97
0.67
3
GAIN
2
1
2
79350186
79350347
2
0.56
2.10
23
UBCNA
8
3
5
1
1
18.07
0.56
18
HLAMP
10
8
2
80801346
88999476
79
0.59
0.17
5
GAIN
3
1
2
1
1
3.03
0.66
3
GAIN
2
1
2
96780716
101656726
52
0.66
0.93
18
UBCNA
7
2
5
1
1
6.76
0.71
7
HLAMP
5
2
2
101874442
114501242
49
0.56
0.36
8
BCNA
4
2
2
1
1
3.81
0.59
4
AMP
2
2
2
115822286
120439282
34
0.72
-0.19
2
NLOH
2
0
2
1
1
1.87
1.00
2
NEUT
2
0
2
121744225
125192068
5
0.52
0.44
11
UBCNA
5
2
3
1
1
4.14
0.53
5
HLAMP
3
2
2
127808226
128180872
15
0.74
-0.14
2
NLOH
2
0
2
1
1
2.01
1.00
2
NEUT
2
0
2
128253571
149520186
118
0.54
0.34
8
BCNA
4
2
2
1
1
3.70
0.56
4
AMP
2
2
2
152267072
171260797
174
0.73
-0.19
2
NLOH
2
0
2
1
1
1.85
1.00
2
NEUT
2
0
2
171300575
171508262
3
0.56
0.14
5
GAIN
3
1
2
1
1
2.94
0.61
3
GAIN
2
1
2
171693455
189940142
159
0.62
0.79
14
UBCNA
6
2
4
1
1
5.93
0.67
6
HLAMP
4
2
2
191770078
192228444
5
0.77
1.05
17
ASCNA
7
1
6
1
1
7.56
0.85
7
HLAMP
6
1
2
196889180
242814009
433
0.73
-0.18
2
NLOH
2
0
2
1
1
1.90
1.00
2
NEUT
2
0
The text was updated successfully, but these errors were encountered:
Sorry, there must be a bug in the string notation after correction. If you look at the Corrected_MinorCN, it is still equal to 0 and Corrected_MajorCN is 2, so that would still mean NLOH. I will push a patch for this. In the meantime, you can use the Corrected_MinorCN and Corrected_MajorCN. Sorry for the inconvenience.
Hi @gavinha:
I have this region, which seems to be LOH based on GATK-CNV and titan call, however, upon correction it becomes NEUT (
chr2:196889180;242814009
). Guess I am missing something, but correction would adjust for purity and impact HLAMP regions etc, correct?The text was updated successfully, but these errors were encountered: