Development has moved to GitHub: https://github.com/denovogear/denovogear/ If you encounter issues or have questions, please post them at https://github.com/denovogear/denovogear/issues Thanks.
Development has moved to GitHub: https://github.com/denovogear/denovogear/ If you encounter issue or have questions, please post them at https://github.com/denovogear/denovogear/issues Thanks.
Development has migrated to GitHub. Please post your request for help at https://github.com/denovogear/denovogear/issues
Hi, I'm trying to compile denovogear 1.1.1 on CentOS. I believe I have all the dependencies (gcc 7.2.1, CMake 3.11.1, HTSlib 1.8, Eigen 3, Boost 1.67). Here is exactly what I've done, any healp would be greatly appreciated. [aschoenr@bratty apps]$ tar -xvf v1.1.1.tar.gz ... [aschoenr@bratty apps]$ cd denovogear-1.1.1/build/ [aschoenr@bratty build]$ cmake .. -- The CXX compiler identification is GNU 7.2.1 -- The C compiler identification is GNU 7.2.1 -- Check for working CXX compiler: /opt/rh/devtoolset-7/root/usr/bin/c++...
Can you post an issue at https://github.com/denovogear/denovogear/issues and I will...
with parameters --pp_cutoff 0 and rd_cutoff 0 I still get empty output (only vcf...
Also: what version of denovogear are you using?
I think we changed one of the vcf output command line option when we refactired dng...
Hi, The BAM headers look ok at a quick glance, which version of denovogear is this?...
Hello, I I work on trios and I am trying to use denovogear. In our lab we are using...
Hi Avi, I will try to follow that. Thank you VERY much! Xiaoxiao
Another option would be to use samtools 0.1.18 which we have tested extensively.
Hi, As Reed indicated the bcftools API has changed quite a bit recently, Could you...
Thank you Avi samtools/1.2/gcc.4.4.7 denovogear-v1.1.1
samtools/1.2/gcc.4.4.7
Hello Reed, Could you tell me how to fix it? Here is my command I used: samtools...
Hi, Which version of samtools is this? Avi
Hello Avi, I try to run denovo gear, but it failed. Here is the error messages: <mpileup>...
Try bcftools view on the BCF file.
Hello, Could you tell me how to fix it ? Thank you! Xiaoixao
Thank you for your helps, and could you tell me how to check the column names in...
What are the column names in your BCF file?
Hi Avinash, I got the same error, but I have the same in the two files. Created paired...
Hi, This error indicates that the sample names in the BCF file and the sample names...
Hello, I am trying to run denovogear for trio analysis, I started with three .bam...
It sounds like you are using a bcf file that is not supported by the dnm module....
Hi, Sorry for the extremely slow response. Would it be possible for you to provide...
Hi Tracy, Good question and sorry for the slow response, I should mention that we've...
Hi Tracy The mapping and base qualities are used by samtools in calculating the genotype...
I've sent Rena a copy of the updated code, thanks for helping debug this !
This has been addressed in this pull-request, https://github.com/denovogear/deno...
Thanks for helping debug Rena, turns out this was a memory issue. DNG upto version...
Thanks for helping debug Rena, turns out this was a memory issue. DNG upto version...
Hi Rena, Could you post the full command that you tried ? Also would it be possible...
Hi Laurent, Sorry for the delay in getting back. Were you able to figure this out...
Hi Stephen, We do not have a Y specific model yet. But for now one possible strategy...
Hi Tracy, The denovogear model does look at all possible genotype configurations...
Hi Tracy, The denovogear model does look at all possible genotype configurations...
Hi, Would it be possible for you to estimate the mutation rate for your species ?...
Can you send us a list of the sites that you are calling on the X? In the meantime,...
It depends on the goals of the analysis. If you have the resources to do this, I...
The background for this error message is described in the documentation for DNG....