Support for heterozygous/homozygous genotype categories?

[jpcartailler]

Greetings,

I found BnpC is while testing out infSCITE and think it might help us with deciphering our SCS data. I have an initial question - according to the docs All matrix entries must be of the following: 0|1|3/" ", where 0 indicates the absence of a mutation, 1 the presence, and a 3 or empty element a missing value..

I'm interested in running our categorical genotype data, which is very similar to your input requirements:

Our input	BnpC input
0-reference	0 indicates the absence of a mutation
1-heterozygous mutation	1 the presence
2-homozygous mutation	1 the presence
3-unknown	3 or empty element a missing value

Is there any facility, or plans, on including hetero/homozygous genotype distinction in BnpC?

Thanks!
JP

[NBMueller]

Hey JP,
Thanks for the interest in our method. So far, BnpC supports only binary data, not incorporating zygosity. It's on the todo list, but short term we are busy polishing it as it is.
Depending on what you are interested in, you could turn the homozygous to heterozygous states and run BnpC. Alternatives incorporating zygosity are SCG (Roth et al.) and SiCloneFit (Zafar et al.), but in our hands, SCG predicts genotypes worse than BnpC and SiCloneFits' runtime is extremely long (for small data size, however, it's worth giving it a try).
Best,
Nico

[jpcartailler]

Hi Nico,

Thanks for the feedback and suggestions, we're currently working our data "converted" to binary, and see what that tells us. If you need help testing/documenting, please don't hesitate to ask. Best regards and thanks so much for all of your efforts!

JP