Varscan Copy Number Calling Workflow: Using Mergesegments.Pl After Cbc
Entering edit mode
8.7 years ago
enabieva ▴ 50

I am trying to identify copy number variation in tumor/normal data using the workflow on the VarScan page. I got as far as the last step, where I got stuck on input to says that it requires the following fields in the input:

USAGE: [segments] OPTIONS
        segments - A segments file with p-values from the DNAcopy library. This should be tab- or space-delimited
        with a header and the following columns: ID, chrom, loc.start, loc.end, num.mark, seg.mean, bstat, pval, lcl, ucl.

Meanwhile, the R script given on the workflow page produces a file with only the following fields:

ID      chrom   loc.start       loc.end num.mark        seg.mean

(even if I write out all columns of segs$output, where segs is the result of calling the segment function in DNAcopy)

My question is: where and how do I get the remaining coumns (bstat, pval, lcl, ucl) for input to

varscan copynumber • 4.9k views
Entering edit mode
8.6 years ago
Irsan ★ 7.4k

When you run the segments.p method from DNAcopy on a DNACopy-class object (that is returned by segments(...)) a data frame containing p-values is returned

segments.p(segs, ngrid=100, tol=1e-6, alpha=0.05, search.range=100, nperm=1000)

also see reference manual for DNACopy page 13-14

Entering edit mode

After I ran the segments.p. I tried to run the Use of uninitialized value $input in <handle> at ../../ line 446. readline() on unopened filehandle at ../../ line 446. Can't use an undefined value as a symbol reference at ../../ line 456.

Anybody got a similar error?

Entering edit mode this helped me, just make a ref-arm-sizes file from the data in the last comment (note that the file should be tab-delimited.) which you can use in the --ref-arm-sizes option in I personally had to add chr before the chrom. number


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