error with genotype function

[amr15]

Hi,
Do you have any suggestions on the following error popping up after running the genotype function in the pileup_and_phase.R script?

Error in as.list.default(X) :
no method for coercing this S4 class to a vector

VCF files from cellsnplite seem to be fine.
Thanks!

[teng-gao]

Thanks for reporting this. My best guess is that there was an issue with the bind_rows here:
https://github.com/kharchenkolab/numbat/blob/main/R/genotyping.R#L9-L12
Maybe the objects were not in the right class. To debug, I would manually read in the vcf and check if get_snps(vcf) gives the desired result (a data.frame with SNP information).
Any additional information (how you ran the script, vcf output) would be helpful for me to reproduce the error.