sciClone: Multiple alleles at single position

Question

[fongchunchan]

Hi,

Currently sciClone mutation input data is chr, pos, ref_reads, var_reads, vaf which assumes that we only have one a single mutated allele at a given position.

Is there a way to get sciClone to work with two independent mutations at the same position? Incorporating a reference and allele column could help with distinguishing these two independent events for clustering?

Thanks,

Fong

Answer 1

[Chris Miller]

SciClone doesn't actually care what the position is, and it'd be a nice fix to change the code to reflect that (pull requests welcome). As a quick fix, though, I'd recommend just changing the sciclone inputs to something unique. if your variants look like:

1  123456  A/T
1  123456  A/C

Then in your sciclone input, make them

1 123456      <vaf info...>
1 1234569999  <vaf info...>

or even

1     123456  <vaf info...>
asdf 123456  <vaf info...>