Description of outputs

Output Files:

TiN_estimate: tumor in normal estimate.

TiN_estimate_CI: confidence interval around tumor in normal estimate.

TiN_hets_aSCNA_model: Copy number data used in TiN estimate.

SSNVs_plot: plot illustrating somatic and germline variants supporting TiN estimate.

TiN_models_plot: TiN posterior distributions for both models and joint.

Kmeans_scatter: Scatter plot of aSCNA data and clustering results.

aSCNAs: Seg file containing the segments used by deTiN. (See description of columns below)

indels: Indels output by deTiN. (See description of columns below)

SSNVs: Somatic single nucleotide variants output but deTiN. (See description of columns below)

Output Columns:

aSCNAs:

f_detin : deTiN's recomputed minor allele fraction after filtering.

f_variance: deTiN's recomputed variance of f_detin.

aSCNA: boolean indicating if deTiN considers this a somatic event.

n_snps_above_mu / n_snps_below_mu : Number of germline SNPs below and above the mean allele fraction.

fishers_p_convergent_seg : probability that the tumor and normal involve copy number changes of different alleles.

TiN_MAP : estimate of TiN based on this segment.

TiN_var : variance of the estimate.

TiN_ci_h / TiN_ci_l : confidence interval on the estimate.

SSNVs / Indels:

tau : Copy number at this locus (defaults to 2 if not covered by seg file).

f_acs : Minor allele fraction (germline SNPs) at this locus (defaults 0.5 if not covered by seg file).

p_somatic_given_TiN : Probability this variant is somatic given the estimate of tumor in normal.

p_outlier : Probability this variant is an outlier given the expected allele fraction and the tumor in normal estimate.