Question: sciClone: Multiple alleles at single position
gravatar for fongchunchan
7 months ago by
fongchunchan10 wrote:


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?



sciclone • 397 views
ADD COMMENTlink modified 3 months ago by Biostar ♦♦ 20 • written 7 months ago by fongchunchan10
gravatar for Chris Miller
7 months ago by
Chris Miller19k
Washington University in St. Louis, MO
Chris Miller19k wrote:

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...>
ADD COMMENTlink written 7 months ago by Chris Miller19k
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