Preprocessing: pp

Functions for loading VCF files, annotating variants, and filtering.

Loading data

pp.load_vcf(vcf_path[, show_progress, ...])

Load a VCF file into an AnnData object.

Annotation

pp.annotate_contexts(adata, fasta_path[, ...])

Annotate variants with trinucleotide contexts.

Filtering

pp.filter_variants(adata[, min_cells, ...])	Filter variants based on presence across cells/samples.
pp.filter_cells(adata[, min_variants, ...])	Filter cells/samples based on number of variants detected.
pp.filter_by_coverage(adata, min_depth[, ...])	Filter variants based on sequencing depth (coverage) across cells/samples.
pp.filter_to_snps(adata[, chrom_prefix, inplace])	Filter to only single nucleotide variants (SNPs).