Reads in Vartrix scSNP pileups. Assumes Vartrix is run in -s coverage mode, outputting barcodes and variants table. If no dir_path is provided, then user must provide individual file paths for each file. If phased VCF and input VCF is provided this function will also remove any non-heterozygous loci, and indels.
Usage
read_vartrix(
dir_path = NULL,
mtx_ref = NULL,
mtx_alt = NULL,
barcodes = NULL,
variants = NULL,
input_vcf = NULL,
phased_vcf = NULL,
verbose = FALSE,
keep_barcodes = NULL,
blacklist = NULL,
min_counts = 1
)Arguments
- dir_path
Path to
Vartrixoutputs directory- mtx_ref
Path to reference allele
.mtxfile- mtx_alt
Path to alternate allele
.mtxfile- barcodes
Path to barcodes file
- variants
Path to variants file
- input_vcf
Germline VCF before phasing
- phased_vcf
Phased VCF
- verbose
Verbosity
- keep_barcodes
Vector of cell barcodes to keep. Will perform an intersect with this list.
- blacklist
Optional blacklist to remove SNPs
- min_counts
Minimum count number across all cells to keep a SNP