Hello,
I have a lots of problems to call CNVs in genome samples (tumor/normal pairs) sequenced with Illumina.
First I tested CNVnator, but I had already problems with the second step, because I don't know the bin_size (./cnvnator -root file.root -chrom ch1 -his bin_size). I tested with 100, 1000, 1000000, but the program ran in all cases just for chromosome 22 over one week and was still not finished. I asked already in another thread for the bin_size, but unfortunally I didn't receive any answers (http://seqanswers.com/forums/showthr...t=11013&page=2).
After that I tested CNV-Seq, but I don't understand the output. Especially I don't know the exact position of the CNV and the difference between log2 and cnv.log2 and the difference between p.value and cnv.p.value
I tried to get some help in another thread (http://seqanswers.com/forums/showthread.php?t=16882) => unfortunally no answer.
Last I tried CNVer, but I can use that tool just for hg18, which doesn't really help me.
I there any other tool, which you can recommend? Or do you have any ideas/suggestions/help to solve the problems with one of the above mentioned tools?
I would be really happy about any comments, because I am completly frustrated.
Thanks a lot in advance.
Robby
I have a lots of problems to call CNVs in genome samples (tumor/normal pairs) sequenced with Illumina.
First I tested CNVnator, but I had already problems with the second step, because I don't know the bin_size (./cnvnator -root file.root -chrom ch1 -his bin_size). I tested with 100, 1000, 1000000, but the program ran in all cases just for chromosome 22 over one week and was still not finished. I asked already in another thread for the bin_size, but unfortunally I didn't receive any answers (http://seqanswers.com/forums/showthr...t=11013&page=2).
After that I tested CNV-Seq, but I don't understand the output. Especially I don't know the exact position of the CNV and the difference between log2 and cnv.log2 and the difference between p.value and cnv.p.value
"chr1" 2250641 2250864 159 100 2250752 0.722575091988798 8.10063503680068e-07 77 448 0.964667045392917 3.93033619539229e-35
"chr1" 2250753 2250976 171 87 2250864 1.02845734551634 3.42115799964058e-11 77 448 0.964667045392917 3.93033619539229e-35
"chr1" 2250865 2251088 161 71 2250976 1.2347180850891 2.18142864565488e-14 77 448 0.964667045392917 3.93033619539229e-35
"chr1" 2250977 2251200 107 60 2251088 0.888124717271795 4.18272787914529e-09 77 448 0.964667045392917 3.93033619539229e-35
"chr1" 2250753 2250976 171 87 2250864 1.02845734551634 3.42115799964058e-11 77 448 0.964667045392917 3.93033619539229e-35
"chr1" 2250865 2251088 161 71 2250976 1.2347180850891 2.18142864565488e-14 77 448 0.964667045392917 3.93033619539229e-35
"chr1" 2250977 2251200 107 60 2251088 0.888124717271795 4.18272787914529e-09 77 448 0.964667045392917 3.93033619539229e-35
Last I tried CNVer, but I can use that tool just for hg18, which doesn't really help me.
I there any other tool, which you can recommend? Or do you have any ideas/suggestions/help to solve the problems with one of the above mentioned tools?
I would be really happy about any comments, because I am completly frustrated.
Thanks a lot in advance.
Robby
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