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Table 1 Characteristics of the six assessed methods

From: Comparison of methods to detect copy number alterations in cancer using simulated and real genotyping data

 

MixHMM

GenoCNA

GPHMM

OncoSNP

ASCAT

GAP

User-definable noise levels

Yes

No

No

No

No

Yes

User-definable LRR copy number means

Yes

No

No

Yes

No

Yes

Automatic LRR shift estimation

No

No

Yes

Yes

Yes

Yes

Automatic contamination estimation

No

Yes

Yes

Yes

Yes

Yes

Germline and somatic LOH distinction

No

No

No

Yes

No

Yes

Maximum copy number

5

4

7

8

?

8

Computation time

Low

Medium

Low

High

Low

Medium