plotting fails

[inijman]

HI,

I'm trying to plot events found in a sample but the script fails with the following error:
***** ERROR: Requested column 4, but database file tmp.$SAMPLE.prev-and-next.windows.bed only has fields 1 - 0.

I've found that this file is actually empty, mainly because of the the awk command in plot_cnv.sh is selecting $4==0 from the models.bed file. In my models files only the values, 3,6 and -1 appear.

How can I fix this?

Best,

[rgcgithub]

Good catch, we haven't updated the plotting script in quite some time. In the short term, you should be able to change it to '$4 >= 0' (-1 indicates a blacklisted window, which is what this is attempting to filter on). I'll push a fix, but the script may need some more attention.

[lakhujanivijay]

Hi

I am looking at this for plotting the CNV results and I am wondering what is this file - sample.cnv.txt ; is this the sample.cnv.bed file which is the output from $CLAMMS_DIR/call_cnv program?

Please help.

[katherinef]

Yes, it takes the sample.cnv.bed.

I think I've noticed another problem with the plot_cnvs.R. It seems to me that the line:
df$max.cn.considered <- ifelse(df$max.cn.considered == 0, 3, -1)
should be:
df$max.cn.considered <- ifelse(df$max.cn.considered >= 0, 3, -1)

Can someone please confirm?

Best wishes

Kath