readSnpMatrix in FACETS gives error

Question

[hsbinf]

Hi! I'm trying to run FACETS (allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing).

I created a SNP matrix using the perl script snp-pileup.pl. But when I run it in R it gives an error.

rcmat <- readSnpMatrix("sample1_facets_input", skip=0L, err.thresh=Inf, del.thresh=Inf, perl.pileup=TRUE) 
Error in scan(filename, what = list(Chromosome = "", Position = 0, NOR.DP = 0,  : 
scan() expected 'a real', got 'chr1'

Any ideas why? I can run most of the samples, its just 1 sample that has this error.

Thanks!

[Kevin Blighe]

Just a guess: in that particular sample, your chromosomes have the 'chr' prefix, when they should be just encoded numerically,. Strip the 'chr' prefix from the input file and then retry.

Kevin