Dna.filter_variants

Dna.filter_variants(min_dp=10, min_gq=30, vaf_ref=5, vaf_hom=95, vaf_het=35, min_prct_cells=50, min_mut_prct_cells=1)

Find informative variants.

This method also adds the NGT_FILTERED layer to the assay which is a copy of the NGT layer but with the NGT for the cell-variants not passing the filters set to 3 i.e. missing.

Parameters

min_dpint

The minimum depth (DP) for the call to be considered. Variants with less than this DP in a given barcode are treated as no calls.

min_gqint

The minimum genotype quality (GQ) for the call to be considered. Variants with less than this GQ in a given barcode are treated as no calls.

vaf_reffloat [0, 100]

All reference calls (NGT = 0) with VAF > vaf_ref are converted to no calls (NGT = 3) for each barcode and variant in the NGT matrix

vaf_hetfloat [0, 100]

All hetrozygous calls (NGT = 1) with VAF < vaf_het are converted to no calls (NGT = 3) for each barcode and variant in the NGT matrix

vaf_homfloat [0, 100]

All homozygous calls (NGT = 2) with VAF < vaf_hom are converted to no calls (NGT = 3) for each barcode and variant in the NGT matrix

min_prct_cellsfloat [0, 100]

The minimum percent of total cells in which the variant should be present (NGT ∈ {0, 1, 2}) after the filters are applied.

min_mut_prct_cellsfloat [0, 100]

The minimum percent of the total cells in which the variant should be mutated, (NGT ∈ {1, 2}) after the filters are applied.

Returns

numpy.ndarray