CNV-seq, to detect Copy Number Variation using next-generation sequencing

[DineshCyanam]

Originally Posted by parveendabas

Thank you dinesh. But my data is not normal/control type and neither its related to 1000 genome project. Its one sample data. What should i do??

Well you still need to compare it with against a normal. See post #9 above.
http://seqanswers.com/forums/showthread.php?p=40537

or

try CNVnator from Mark Gerstein's lab. You don't need to supply a ref file for CNVnator. More info and link to papers here: http://sv.gersteinlab.org/

[difereg]

Hello!
Does the CNV-seq be used in genome (sequenced by Illumina -Short reads) in haploids apicomplexa?
Any thoughs?
Thanks a lot.
difereg

[findingdan]

Originally Posted by mimi_lupton

Dear all,
I have a couple of questions regarding CNV-seq.
I am having a play around with some DNA sequencing that is from custom capture. I have analysed some BAM files using the program. Some work fine, but some file combinations come up with an error, which is strange as all the data has been produced and analysed in exactly the same way. The error is;

"Can't use an undefined value as an ARRAY reference at /share/apps/cnv-seq_1.0/bin/cnv-seq.pl line 204, <REF> line 6460211."

I think this is some kind of Perl script error??

Also does anyone have any experience of using capture data with CNV-seq? any advice would be greatly appreciated.

Thanks for you help

Ever get an answer for this 'value as an ARRAY reference" problem? i'm having the same issue..

[adurasiwam3]

I'm running the CNV-seq package and I keep getting the following error:

write read-counts into file: test.hits-vs-ref.hits.log2-0.6.pvalue-0.001.count
R package cnv output: test.hits-vs-ref.hits.log2-0.6.pvalue-0.001.minw-4.cnv
Error in library(cnv) : there is no package called 'cnv'
Execution halted

Can someone please help me out?

Btw, the data I'm using is the sample data available on the CNV-seq website.

Thank you

[pd]

While running CNV-seq, sometimes it works perfectly but sometimes i end with the following error "Can't use an undefined value as an ARRAY reference at line 205, <REF> line 1119928258".
The same has been asked many a times but no solution yet. Anyone to help out or some other suggestion for alternate CNV detection algorithms?

[ragowthaman]

@adurasiwam3:
It indicates, you dont have the CNV R package installed into correct place (or at all).

Assuming your machine has R.
you install the package by issuing following command while inside the package's root folder.

R CMD INSTALL /cnv/

If your syestem's R is not in the path, you need to call it explicitly (eg. /apps/bin/R) instead of R.

Hope this helps.

[adurasiwam3]

it helped!

thank you ragowthaman

[adurasiwam3]

can someone explain how the sensitivity/specificity for CNV-seq is calculated in the CNV-seq paper?

Where can I get data with simulated CNVs (including the known positions)?

Thank you!

[billthebrute]

Hi CNV-seq users. I am having a bit of trouble understanding how the cnv caller works.

The results of one of my .cnv files is as follows:


"22" 16275937 18988591 204 2822 17632264 -0.683143010100174 2.46090424342812e-08 0 NA NA NA
"22" 17632265 20344919 195 3190 18988592 -0.925076474377026 2.85143491959854e-12 0 NA NA NA
"22" 18988593 21701247 191 3107 20344920 -0.916943777560497 3.8950753868117e-12 0 NA NA NA
"22" 20344921 23057575 188 3082 21701248 -0.928128374311553 2.53633054795169e-12 0 NA NA NA
"22" 21701249 24413903 210 3108 23057576 -0.780591350215992 6.85565176334874e-10 0 NA NA NA
"22" 23057577 25770231 206 3256 24413904 -0.875450536557434 1.90371570869566e-11 0 NA NA NA
"22" 24413905 27126559 177 3139 25770232 -1.04154984297352 3.22421238629005e-14 0 NA NA NA
"22" 25770233 28482887 180 3103 27126560 -1.00066096467345 1.55775796481263e-13 0 NA NA NA
"22" 27126561 29839215 157 2718 28482888 -1.00677507135017 1.23086398489238e-13 0 NA NA NA
"22" 28482889 31195543 143 2606 29839216 -1.08081611126415 7.11362307806884e-15 0 NA NA NA
"22" 29839217 32551871 160 2852 31195544 -1.04889625103093 2.42971963892229e-14 0 NA NA NA
"22" 31195545 33908199 155 2827 32551872 -1.08199784203134 6.7976211176428e-15 0 NA NA NA
"22" 32551873 35264527 166 2610 33908200 -0.867860739584727 2.5422391389699e-11 0 NA NA NA
"22" 33908201 36620855 170 2621 35264528 -0.839576781665121 7.44538364328285e-11 0 NA NA NA
"22" 35264529 37977183 210 3210 36620856 -0.827178143817948 1.19029886619997e-10 0 NA NA NA
"22" 36620857 39333511 218 3208 37977184 -0.772340181152399 9.32704407763649e-10 0 NA NA NA
"22" 37977185 40689839 195 2891 39333512 -0.783088659201844 6.24484354174541e-10 0 NA NA NA
"22" 39333513 42046167 191 2608 40689840 -0.664365405669734 4.82741849789952e-08 0 NA NA NA
"22" 40689841 43402495 306 4365 42046168 -0.727444175298556 4.90998416767461e-09 0 NA NA NA
"22" 42046169 44758823 409 5386 43402496 -0.612107561034328 3.04270126227705e-07 0 NA NA NA
"22" 43402497 46115151 273 3718 44758824 -0.660619993474034 5.51777958936528e-08 0 NA NA NA
"22" 44758825 47471479 193 3190 46115152 -0.939949750858556 1.61095440200424e-12 0 NA NA NA

Surely this should have been annotated as a cnv as there are more than 4 windows with a log2<-0.6 and high significance !
Moreover I find the coordinates strange:
look at the first and third line:
"22" 16275937 18988591
"22" 18988593 21701247

18988591 is not equal to 18988593. Whereas sometimes, if I change the window size the end of the first line and the beginning of the third would be the same.

These files were created with default values, window size = 2712655

Thanks in advance for any insight you can give me. I am tempted to call the cnvs manually...what would be the best way to do so from the .cnv file ?

[jterol]

Hi!
I've got a chromosome with 3 deletions and woudl like to have them all in the same plot, but it seems I can only choose 1 CNV at a time:
>plot.cnv(data, CNV=2, upstream=2e+6, downstream=2e+6)

Any suggesion?

[jordiet]

Originally Posted by jterol

Hi!
I've got a chromosome with 3 deletions and woudl like to have them all in the same plot, but it seems I can only choose 1 CNV at a time:
>plot.cnv(data, CNV=2, upstream=2e+6, downstream=2e+6)

Any suggesion?

Hi

in the R package for the cnv-seq (cnv-seq manual) there is a function to do it:

plot.cnv.chr <- function (data, chromosome = NA, from = NA, to = NA, title = NA, ylim = c(-4, 4), glim = c(NA, NA), xlabel = "Position (bp)")

Unfortunately I've tried to use it several times and I couldn't get it...

Let me know if you get it!

[jterol]

Well,

after some struggling I executed:
>plot.cnv(data, ylim = c(-2,2))
And got all the deletions and the whole chromosome, and even managed to limit the log2(ratio) to the ones I wanted. So the trock was not to choose any CNV!

[Ayush_Saxena]

Is there any way we can report a bug for CNV-Seq, I tried searching for it but couldn't find.

the software, for some strange reasons is not calling CNVs even when all conditions are met. I used a log2 threshold of 0.8 and a window size of only 2 so that I can look at the result(cnv.print()) by eye and judge which ones to pick.

"CHROMOSOME_II" 1450045 1451171 404 416 1450608 0.881401332001257 2.29121717076986e-13 0 NA NA NA
"CHROMOSOME_II" 1450609 1451735 570 464 1451172 1.22046668131509 1.31845290945157e-22 0 NA NA NA
"CHROMOSOME_II" 1451173 1452299 629 550 1451736 1.11725796585782 1.18360892978282e-19 0 NA NA NA
"CHROMOSOME_II" 1451737 1452863 671 657 1452300 0.954048963268409 3.24101505961822e-15 0 NA NA NA
"CHROMOSOME_II" 1452301 1453427 602 577 1452864 0.984821735504775 5.02877099034994e-16 0 NA NA NA
"CHROMOSOME_II" 1452865 1453991 513 516 1453428 0.915217327574355 3.2389370038797e-14 0 NA NA NA
"CHROMOSOME_II" 1453429 1454555 590 516 1453992 1.1169734562165 1.20564598087743e-19 0 NA NA NA
"CHROMOSOME_II" 1453993 1455119 551 465 1454556 1.16845116996632 4.16186035989176e-21 0 NA NA NA
"CHROMOSOME_II" 1454557 1455683 374 369 1455120 0.943047021217795 6.25787394726544e-15 0 NA NA NA
"CHROMOSOME_II" 1455121 1456247 415 422 1455684 0.899497904917657 8.08876111589643e-14 0 NA NA NA
"CHROMOSOME_II" 1455685 1456811 615 573 1456248 1.02568083886025 4.03369375071261e-17 0 NA NA NA
"CHROMOSOME_II" 1456249 1457375 666 575 1456812 1.13558978863008 3.59196486144447e-20 0 NA NA NA
"CHROMOSOME_II" 1456813 1457939 663 565 1457376 1.15438757020059 1.04963378485956e-20 0 NA NA NA
"CHROMOSOME_II" 1457377 1458503 609 524 1457940 1.14050498375944 2.60576418573692e-20 0 NA NA NA
"CHROMOSOME_II" 1457941 1459067 410 408 1458504 0.930684324924505 1.30371091397085e-14 0 NA NA NA

This entire >8kb region qualifies all conditions set for a CNV to be called and its still not called which makes me a little skeptical about the software itself. Can anyone list some other reliable alternatives

[Ayush_Saxena]

Originally Posted by billthebrute

Hi CNV-seq users. I am having a bit of trouble understanding how the cnv caller works.

The results of one of my .cnv files is as follows:


"22" 16275937 18988591 204 2822 17632264 -0.683143010100174 2.46090424342812e-08 0 NA NA NA
"22" 17632265 20344919 195 3190 18988592 -0.925076474377026 2.85143491959854e-12 0 NA NA NA
"22" 18988593 21701247 191 3107 20344920 -0.916943777560497 3.8950753868117e-12 0 NA NA NA
"22" 20344921 23057575 188 3082 21701248 -0.928128374311553 2.53633054795169e-12 0 NA NA NA
"22" 21701249 24413903 210 3108 23057576 -0.780591350215992 6.85565176334874e-10 0 NA NA NA
"22" 23057577 25770231 206 3256 24413904 -0.875450536557434 1.90371570869566e-11 0 NA NA NA
"22" 24413905 27126559 177 3139 25770232 -1.04154984297352 3.22421238629005e-14 0 NA NA NA
"22" 25770233 28482887 180 3103 27126560 -1.00066096467345 1.55775796481263e-13 0 NA NA NA
"22" 27126561 29839215 157 2718 28482888 -1.00677507135017 1.23086398489238e-13 0 NA NA NA
"22" 28482889 31195543 143 2606 29839216 -1.08081611126415 7.11362307806884e-15 0 NA NA NA
"22" 29839217 32551871 160 2852 31195544 -1.04889625103093 2.42971963892229e-14 0 NA NA NA
"22" 31195545 33908199 155 2827 32551872 -1.08199784203134 6.7976211176428e-15 0 NA NA NA
"22" 32551873 35264527 166 2610 33908200 -0.867860739584727 2.5422391389699e-11 0 NA NA NA
"22" 33908201 36620855 170 2621 35264528 -0.839576781665121 7.44538364328285e-11 0 NA NA NA
"22" 35264529 37977183 210 3210 36620856 -0.827178143817948 1.19029886619997e-10 0 NA NA NA
"22" 36620857 39333511 218 3208 37977184 -0.772340181152399 9.32704407763649e-10 0 NA NA NA
"22" 37977185 40689839 195 2891 39333512 -0.783088659201844 6.24484354174541e-10 0 NA NA NA
"22" 39333513 42046167 191 2608 40689840 -0.664365405669734 4.82741849789952e-08 0 NA NA NA
"22" 40689841 43402495 306 4365 42046168 -0.727444175298556 4.90998416767461e-09 0 NA NA NA
"22" 42046169 44758823 409 5386 43402496 -0.612107561034328 3.04270126227705e-07 0 NA NA NA
"22" 43402497 46115151 273 3718 44758824 -0.660619993474034 5.51777958936528e-08 0 NA NA NA
"22" 44758825 47471479 193 3190 46115152 -0.939949750858556 1.61095440200424e-12 0 NA NA NA

Surely this should have been annotated as a cnv as there are more than 4 windows with a log2<-0.6 and high significance !
Moreover I find the coordinates strange:
look at the first and third line:
"22" 16275937 18988591
"22" 18988593 21701247

18988591 is not equal to 18988593. Whereas sometimes, if I change the window size the end of the first line and the beginning of the third would be the same.

These files were created with default values, window size = 2712655

Thanks in advance for any insight you can give me. I am tempted to call the cnvs manually...what would be the best way to do so from the .cnv file ?

I overlooked your post before I posted mine, I'm having a very similar problem and I've also posted my data. Did you get around your problem or called manually?