Table 1 Names, default values, and validity range of the interface parameters for a given mean mapped read depth C

Alternate counts (field 3.1)

2

\(1 < x \ll C/2\)

Higher values select events with more supporting ALT reads and remove PCR errors, but bias the results toward high CN/expressed genes.

MAF (field 3.2)

0.01

\(0 \le x < 0.5\)

Smaller values imply more rare events compared to the reference population.

Variant Frequency (field 3.3)

0.01

\(0 < x \le 1\)

Smaller values include less common mutations among cells in the experiment.

Minimum depth (field 4.1)

3

\(0 \le x \ll C\)

Bigger values imply more NA sites per time point.

Max missing value (field 4.2)

0.4

\(0\le x\le 1\)

Higher values keep mutational sites for which larger number of cells has an NA value.

Minimum median depth (field 4.3)

8

\(1\le x \lesssim C\)

Bigger values keep only loci with bigger median coverage among cells.

Minimum alt median depth (field 4.4)

4

\(1\le x \lesssim C\)

Bigger values keep only mutations with more supporting reads in the cell population.

Learning rate (field 5.1)

1

Higher values permit to avoid local minima, but are less accurate.

False positive rates (field 5.2)

\(0<x<1\)

Lower values imply more constraining data values.

False negative rates (field 5.3)

\(0<x<1\)

Lower values imply more constraining data values.

MCMC iterations (field 4.4)

10000

\(x>1\)

Number of restart (field 5.5)

50

\(x\ge 1\)

Early stopping (field 5.6)

500

\(x>1\)