SMC-Het Challenge Entry:

This is a CWL workflow which was submitted to the SMC-Het Challenge.

Example and reference data files can be found here.

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Resource Usage

This method was part of the medium memory group

high memory = +100GB RAM medium memory = +64GB RAM low memory = <64GB RAM

Details

Challenge participants were asked to complete a quiz to describe some of the details about their entry:

Is your method probabilistic?

probabilistic

How do you perform inference?

em

What sort of prior do you put on the parameters of your model?

data

Do you cluster CNAs? SNVs? SVs? Indels? (Check all that apply)

snv

If you use CNAs in your inference do you use clonal CNAs only or do you also use subclonal CNAs?

clonal

If you use CNAs, do you use total CN only or do you use allele specific copy numbers?

allelespecific

Do you correct for cancer cell fraction?

yes

Do you predict mutation multiplicities?

yes

Do you cluster all mutations at once or do you do post hoc assignment?

yes

How do you choose the number of clusters?

pllh

Do you assume "weak parsimony" (i.e. that mutations in the same cluster are in the same cell)?

no

Do you attempt to infer the phylogeny of the tumour?

no

Does your method make any of these assumptions? (Check those that apply)

infinite_sites

What noise model do you use for Variant Allele Fractions?

binomial

Is the source code for your method available? If yes, please provide a link to where the code is available.

yes

What is the peer-reviewed publishing status of your method? If it has been published please provide a DOI or PMID.

notyet

Has a description of your method appeared in a non-peer-reviewed format? If yes, please provide a link.

website