When I use sequenza to call CNV for WES,Error pops out.

Question

[zhaolianhe1992]

I had actually tried to run sequenza.extract on seqz.data but receive an error:

> test <- sequenza.extract(seqz.data)
Error in pipe(paste("gzip -d -c", file, "| cut -f 1,6,10")) : invalid 'description' argument

Can anyone explain this to me in a bit further detail? Is there just something wrong with my data files or am I just making a poor assumption on what sequenza is actually doing? If sequenza.extract(data.file) is correct for real data then what purpose does the GC normalization steps serve?

Thank you

[Q.S.Yang]

hi,have you solved the problem?

Answer 1

[favero]

Hi, sorry I haven't seen this until now!

You probably need to use Rtools (which include a set of common unix command for windows to run within R)

Look here: https://cran.r-project.org/bin/windows/Rtools/

Answer 2

[Q.S.Yang]

> gz1 <- gzfile(“sample.seqz.gz","w” )
> write.table(seqz.data, gz1, col.names = T, row.names=F, sep = “\t”, quote = F)
> close(gz1)
> gc.stats <- gc.sample.stats(“sample.seqz.gz", gz=FALSE)

This can solve the same problem.