how to properly run TrioCNV for trios CNV detection

Question

[giusdalt95]

Hi, everybody I am trying to run TrioCNV on a trio, in order to detect inherited Copy Number Variants (CNVS), following the tutorial at this link. I ran the preprocessing command ad indicated in the tutorial, but the resulting output is a file with only a row (apparently an header) as follows:

CHROM START END GR2108p GR2108m GR2108 GC Mappability

and it gives me error when i run the subsequent calling command. I don't know which is the mistake, and the only explanation is that pedigree and mappability files are not properly formatted. I'm using the same map file that authors used (available here); the pedigree file is formatted ad follows:

FAM001  GR2108  GR2108p GR2108m 1       2
FAM001  GR2108p 0       0       1       1
FAM001  GR2108m 0       0       2       1

where the three rows represent the proband, the father and the mother respectively. Unluckily, on github such tool is poorly explained, and apparently very few people use it. Could anybody give me some advice? Thank you in advance, Giuseppe

[German.M.Demidov]

It is very difficult to help not having an error message and this is maybe not a well known tool

I can't say that I promote trio mode in ClinCNV, but I actually do

https://github.com/imgag/ClinCNV

--triosFile

flag specified + csv with trios should do the job

[giusdalt95]

Thank you so much... i will post the error here, but actually my doubt was that mappability and pedigree files were improperly formatted. However, is a poorly known tool, and thank you again for the hint!

So, this is what I type:

java -jar TrioCNV.jar call \
--input TrioCNVDir/trio_ \
--pedigree russo.ped \
--mappability wgEncodeCrgMapabilityAlign100mer.bigWig \
--output test.txt

and here comes what I get:

INFO  2021-05-31 15:25:48 TrioCNV - Checking R environment and packages ......
INFO  2021-05-31 15:25:49 TrioCNV - Estimating parameters ......
INFO  2021-05-31 15:25:51 TrioCNV - HMM Segmentation ......
Exception in thread "main" java.lang.NullPointerException
    at cn.edu.hit.triocnv.module.TrioCall.runMultiThreads(TrioCall.java:122)
    at cn.edu.hit.triocnv.cmdline.TrioCNV.run(TrioCNV.java:89)
    at cn.edu.hit.triocnv.cmdline.TrioCNV.main(TrioCNV.java:40)

[German.M.Demidov]

yeap, null pointer exception. something refers to something which is not defined.

https://stackoverflow.com/questions/218384/what-is-a-nullpointerexception-and-how-do-i-fix-it

It is not easy to debug this. You can go to the TrioCNV file and check what happens on line 122 (some multli-threading problem?)

add some print-outs to the file https://github.com/yongzhuang/TrioCNV/blob/master/src/main/java/cn/edu/hit/triocnv/module/TrioCall.java to understand at which exactly line problem happen, it may allow you to understand where exactly it happens