Hi,

I am working with whole exome data, and I am trying to follow this pipeline in order to get a CNV analysis. When I reach the segments.pl step, I am able to get an output, but the end of every chromosome happens to have NA value in the last 4 columns .

This is part of the output

ID chrom loc.start   loc.end num.mark seg.mean     bstat         pval       lcl       ucl
1  X30     1     69445 249211976    20269   0.2667        NA           NA        NA        NA
2  X30     2     41347  21266186      955  -0.0224  7.877737 5.703810e-13  21265217  21266186
3  X30     2  21360274  21364172        6   1.4990  8.077258 1.906060e-13  21364172  21585074
4  X30     2  21585074 140426651     7026  -0.0006  6.685767 5.260426e-09 140426103 140426651
5  X30     2 140990738 141004571        4   1.5195  9.203246 1.189773e-17 141004571 141026628
6  X30     2 141026628 243037012     7369   0.0425        NA           NA        NA        NA

I would like to ask for the possible reason this is happening. Also, I feel I shouldn't remove those columns, but getting a proper value out of them. I tried to change (just to try) the loc.end of the last segment of one chromosome to the "last base" of the chromosome (for example, the last segment of chromosome 2 ends in 243037012 so I changed it to see what happened if it was 243199373 instead), to see if the length of this last segment was the problem, but I still got NA values.

I will thank any help or advice!