Dna.filter_variants

Dna.filter_variants(min_dp=10, min_gq=30, min_vaf=20, max_vaf=100, min_prct_cells=50, min_mut_prct_cells=1, min_std=0)

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.

min_vaffloat [0, 100]

If the VAF of a given variant for a given barcode is less than the given value, and the call is ‘1’ i.e. HET, then it is converted to a no call.

max_vaffloat [0, 100]

If the VAF of a given variant for a given barcode is greater than the given value, and the call is ‘1’ i.e. HET, then it is converted to a no call.

min_prct_cellsfloat [0, 100]

The minimum percent of total cells in which the variant should be called as ‘0’, ‘1’, or ‘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, i.e., either ‘1’ or ‘2’ after the filters are applied.

min_stdfloat [0, 100]

The standard deviation of the VAF across the cells of the variants should be greater than this value.

Returns

numpy.ndarray