statistical model for finding anomalous genotype cells in mixed genotype scRNAseq data
static binary for linux x64/x86 included in main directory python version is now depricated
usage: ./cellector_linux -h
cellector 1.0.0
Haynes Heaton <[email protected]>
genotype outlier detection for scRNAseq
USAGE:
cellector [OPTIONS] --alt <alt> --ref <ref> --barcodes <barcodes> --output_directory <output_directory>
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
OPTIONS:
-r, --ref <ref> ref.mtx matrix from vartrix
-a, --alt <alt> alt.mtx matrix from vartrix
-v, --vcf <vcf>
vcf associated with the alt.mtx and ref.mtx, only required to associated loci with variants and to get the
genotypes of the minority and majority cells in a vcf output
-b, --barcodes <barcodes> cell barcodes
-g, --ground_truth <ground_truth>
cell hashing assignments or other ground truth, first column barcodes second column assignment
--interquartile_range_multiple <interquartile_range_multiple>
number of interquartile range multiples away from 25th percentile to make the threshold to call an outline
--min_alleles_posterior <min_alleles_posterior>
minimum number of alleles for both minority distribution and majority distribution to have for a locus to be
used for posterior probability calculation
--min_alt <min_alt>
minimum number of cells containing the alt allele for the variant to be used for clustering (default 4)
--min_ref <min_ref>
minimum number of cells containing the ref allele for the variant to be used for clustering (default 4)
--output_directory <output_directory>
output directory where other output files will be stored
--posterior_threshold <posterior_threshold>
posterior probability threshold for assignment of minority or majority (default 0.999)