I have made a cancer genome simulator which produces two tracks:

• Read depth track (one for control sample and one for tumor sample)
• B-allele fraction for heterozygous SNPs track

The whole idea of making this simulator was to have a gold standard for benchmarking different somatic copy number variation detection algorithms. However, after compiling a long list of available algorithms, none uses as input such tracks. Some of the algorithms use the pileup file format for input. That is why I was thinking if I could use the data shown here and construct a pileup file so that other algorithms can run on the simulated data. Any idea is much appreciated.

They output of each track looks like this:

Read depth track:

fixedStep    chrom=chrY    start=0    step=1000
0
0
0
0
0
1
203
249
233
297
299
345
314
346

B-allele fraction for heterozygous SNPs track:

track graphType=points viewLimits=0:1 windowingFunction=none
variableStep    chrom=chrY    
1934     NaN
1987     NaN
3830     NaN
6251     NaN
6726     NaN
7470     NaN
8634     NaN
9229     0.34375
9678     0.59375
9714     0.46875
11431    0.578947368421
14188    0.675
15318    0.577777777778
16291    0.690476190476
16297    0.428571428571
19140    NaN