Cnvnator Output File

Question

[madkitty]

Can anyone explain to me the output file of CNVnator ? I don't understand what are column 1,2 and3 at the end. In the Readme file it doesn't say anything about the last 3 columns.

TYPE    COORDINATE SIZE NormalizedRD    P-val1    P-val2    COL1    COL2    COL3
deletion    chr1:..-..    5700    0.477551    2.25E-07    1.19E+09    0.00326981    1.62E+09    1
deletion    chr1:..-..    14400    0.398247    1.11E-11    2.87E+09    1.29E-11    2.87E+09    1
deletion    chr1:..-..    2300    0.383089    4.78E-05    67.6142    20065.7    18627.1    1
deletion    chr1:..-..    1500    0.220024    3.39E-06    5.76E-10    1    1    1
deletion    chr1:..-..    1000    0.21195    0.00105391    4.98E-06    1    1    1

Thanks :)

[NB]

Can you please tell me how do u view the output files from CNVnator ? I ran CNVnator and got a .root file and tried to open it in the ROOT package - all I got were some graphs. How can we view the text file ? Thanks!

[Chris Fields]

You have a few choices:

1. Use CNVnator's built in visualization (describe in the README)
2. Convert the data to VCF, add in the reference data sequence, and then use a tool like IGV

Answer 1

[Chris Fields]

The output is pretty clearly defined in the README:

CNV_type coordinates CNV_size normalized_RD p-val1 p-val2 p-val3 p-val4 q0

normalized_RD -- normalized to 1.
p-val1        -- is calculated using t-test statistics.
p-val2        -- is from probability of RD values within the region to be in
the tails of gaussian distribution describing frequencies of RD values in bins.
p-val3        -- same as p-val1 but for the middle of CNV
p-val4        -- same as p-val2 but for the middle of CNV
q0            -- fraction of reads mapped with q0 quality

To have correct output at q0 field one need to use option -unique when extracting read mapping from bam/sam files.

[astulaaa]

I cannot see such option -unique at all. Is it version specific in CNVnator or that's option from some BAM file preprocessing tool before using CNVnator?

Answer 2

[styer.alex]

Has anyone had trouble using the built-in visualization? I get the prompt to enter a specified region, enter the region, and then the prompt comes back (and continues to come back even after trying every format of entry). Like this below:

cnvnator -root my.root -view 100

'>chr11:150988001-150996400

'>11:150988001-150996400

'>11 150988001 150996400

'>chr11 150988001 150996400

'>...and it continues on like this until I have to terminate

If other folks have had this problem and resolved it, your insight would be much appreciated!

[dovi]

If you are using a server you need to ssh with ssh -X, otherwise you can't see the plot.