Question: sciClone: Multiple alleles at single position
gravatar for fongchunchan
19 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 • 654 views
ADD COMMENTlink modified 15 months ago by Biostar ♦♦ 20 • written 19 months ago by fongchunchan10
gravatar for Chris Miller
19 months ago by
Chris Miller20k
Washington University in St. Louis, MO
Chris Miller20k 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 19 months ago by Chris Miller20k
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 768 users visited in the last hour