Could you show me your code of 'cnv_facets.R' script. I found some errors when I run this command:

cnv_facets.R -t tumor.bam -n normal.bam -vcf snps.vcf.gz -o tex

# Load required packages
library(facets)
library(argparse)

# Define the run_facets function
run_facets <- function(tumor_bam, normal_bam, vcf_file, output_prefix) {
    rcmat <- readSnpMatrix(vcf_file, tumor_bam, normal_bam)
    preproc <- preProcSample(rcmat)
    proc <- procSample(preproc, cval = 150)
    fit <- emcncf(proc)

    pdf(paste0(output_prefix, "_facets.pdf"))
    plotSample(proc, fit)
    dev.off()

    write.table(fit$cncf, paste0(output_prefix, "_facets_cncf.txt"), sep = "\t", quote = FALSE, row.names = FALSE)
    write.table(fit$segs, paste0(output_prefix, "_facets_segs.txt"), sep = "\t", quote = FALSE, row.names = FALSE)
}

# Argument parsing
parser <- ArgumentParser(description = 'Run FACETS for CNV calling')
parser$add_argument('-t', '--tumor', required = TRUE, help = 'Tumor BAM file')
parser$add_argument('-n', '--normal', required = TRUE, help = 'Normal BAM file')
parser$add_argument('-vcf', '--vcf', required = TRUE, help = 'SNPs VCF file')
parser$add_argument('-o', '--output', required = TRUE, help = 'Output prefix')
args <- parser$parse_args()

#test function
run_facets(<normal_bam>, <tumour_bam>, <vcf_file>, <output_prefix>)

# Run the function
run_facets(args$tumor, args$normal, args$vcf, args$output)

The error happens on when I run the run_facets function and it is as follows:

Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  scan() expected 'a real', got 'Description="Allfilterspassed">'
5.
scan(file = file, what = what, sep = sep, quote = quote, dec = dec,
nmax = nrows, skip = 0, na.strings = na.strings, quiet = TRUE,
fill = fill, strip.white = strip.white, blank.lines.skip = blank.lines.skip,
multi.line = FALSE, comment.char = comment.char, allowEscapes = allowEscapes, ...
4.
read.table(file = file, header = header, sep = sep, quote = quote,
dec = dec, fill = fill, comment.char = comment.char, ...)
3.
read.csv(filename, stringsAsFactors = FALSE, colClasses = rep(c("character",
"numeric", "character", "numeric"), c(1, 1, 2, 8)))
2.
readSnpMatrix(vcf_file, tumor_bam, normal_bam)
1.
run_facets("LN88_chr19.sorted.bam", "Tail88_chr19.sorted.bam",
"Tail88_chr19.variants.vcf", "cnv_output")

Hi, thanks for providing cnv_facets. I'm using it to analyze hundreds of matched tumor samples for PyClone. I've noticed that the dosage in some spider plots falls off the good fit line. Should I adjust parameters per sample, or is there an accepted threshold? Or could you kindly point me to any resources on this? Many thanks again.