genotype

This module provides auxiliary methods for genotype handling used both by the SNP-IC and cpSNP-IC calculation pipelines. It exposes both a Click CLI group and Python-callable wrappers.

CLI Commands

oddSNP genotype

Usage

oddSNP genotype [OPTIONS] COMMAND [ARGS]...

aggregate-pileup

Aggregate pileup files generated by cellSNP into a single DataFrame

Arguments:

INPATH: Path to the folder containing cellSNP output files. The folder

should contain at least the following files: cellSNP.samples.tsv, cellSNP.tag.AD.mtx, cellSNP.tag.DP.mtx, and cellSNP.tag.OTH.mtx.

OUPATH: Path to the folder to store the aggregated pileup file.

Usage

oddSNP genotype aggregate-pileup [OPTIONS] INPATH OUPATH

Options

--force

Override target file.

Arguments

INPATH

Required argument

OUPATH

Required argument

Python API

oddSNP.genotype.call_aggregate_pileup(inpath, oupath, force)

Python API wrapper for aggregate_pileup().

Parameters:

• inpath – Path to the folder containing cellSNP output files. The folder should contain at least the following files: cellSNP.samples.tsv, cellSNP.tag.AD.mtx, cellSNP.tag.DP.mtx, and cellSNP.tag.OTH.mtx.

• oupath – Path to the folder to store the aggregated pileup file.

• force – If True, override any existing output file.