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 :)
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madkitty
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.
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?
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!
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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!
You have a few choices: