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Corrected NEUT call, which seems to be a region of DLOH instead. #85

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sahilseth opened this issue Jun 10, 2020 · 1 comment
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@sahilseth
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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?

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

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@gavinha
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gavinha commented Jun 10, 2020

Hi @sahilseth

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.

Best,
Gavin

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