Dna.get_variant_bulk_metrics

Dna.get_variant_bulk_metrics#

missionbio.mosaic.dna.Dna.get_variant_bulk_metrics

Dna.get_variant_bulk_metrics(variants=None)#

Metrics for each variant.

Combining this with get_annotations provides equivalent information as the Tapestri Insights v2.2 variants table. The metrics are generated using the NGT_FILTERED, AF, and DP layers of the assay.

Parameters:
variantslist

List of variants for which the metrics are to be generated for (e.g. [‘chr1:12341234:T/A’]). By default it will get annotations for all variants from the assay.

Returns:
variantspandas.DataFrame
A dataframe containing the following values for each variant:

  1. Number of genotyped cells

  2. Number of cells mutated

  3. VAF by cell count

  4. VAF by read count

  5. Number of filtered WT cells

  6. Number of filtered HET cells

  7. Number of filtered HOM cells

  8. VAF of filtered WT cells

  9. VAF of filtered HET cells

  10. VAF of filtered HOM cells

< Class Dna

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