Question: readSnpMatrix in FACETS gives error
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gravatar for hsbinf
2.1 years ago by
hsbinf20
hsbinf20 wrote:

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!

ploidy cnv purity facets • 656 views
ADD COMMENTlink modified 2.1 years ago • written 2.1 years ago by hsbinf20

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

ADD REPLYlink written 2.1 years ago by Kevin Blighe61k
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