Question: Cnvnator Output File
gravatar for madkitty
8.0 years ago by
madkitty600 wrote:

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 :)

ADD COMMENTlink modified 3.1 years ago by styer.alex10 • written 8.0 years ago by madkitty600

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!

ADD REPLYlink written 8.0 years ago by Nandini840

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
ADD REPLYlink modified 7.0 years ago • written 7.0 years ago by Chris Fields2.1k
gravatar for Chris Fields
7.0 years ago by
Chris Fields2.1k
University of Illinois Urbana-Champaign
Chris Fields2.1k wrote:

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.
ADD COMMENTlink written 7.0 years ago by Chris Fields2.1k

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?

ADD REPLYlink written 7 weeks ago by astulaaa0
gravatar for styer.alex
3.1 years ago by
styer.alex10 wrote:

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



'>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!

ADD COMMENTlink written 3.1 years ago by styer.alex10

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

ADD REPLYlink written 3.1 years ago by dovi60
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