Activity for DeNovoGear
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Reed A. Cartwright modified a comment on discussion Help
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.
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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.
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Development has migrated to GitHub. Please post your request for help at https://github.com/denovogear/denovogear/issues
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Anonymous posted a comment on discussion Help
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++...
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Can you post an issue at https://github.com/denovogear/denovogear/issues and I will...
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Anonymous posted a comment on discussion Help
with parameters --pp_cutoff 0 and rd_cutoff 0 I still get empty output (only vcf...
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Also: what version of denovogear are you using?
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I think we changed one of the vcf output command line option when we refactired dng...
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Avinash Ramu posted a comment on discussion Help
Hi, The BAM headers look ok at a quick glance, which version of denovogear is this?...
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Anonymous posted a comment on discussion Help
Hello, I I work on trios and I am trying to use denovogear. In our lab we are using...
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Xiaoxiao posted a comment on discussion Help
Hi Avi, I will try to follow that. Thank you VERY much! Xiaoxiao
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Another option would be to use samtools 0.1.18 which we have tested extensively.
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Hi, As Reed indicated the bcftools API has changed quite a bit recently, Could you...
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Thank you Avi samtools/1.2/gcc.4.4.7 denovogear-v1.1.1
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samtools/1.2/gcc.4.4.7
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Hello Reed, Could you tell me how to fix it? Here is my command I used: samtools...
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Hi, Which version of samtools is this? Avi
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Hello Avi, I try to run denovo gear, but it failed. Here is the error messages: <mpileup>...
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Anonymous posted a comment on discussion Help
Try bcftools view on the BCF file.
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Hello, Could you tell me how to fix it ? Thank you! Xiaoixao
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Thank you for your helps, and could you tell me how to check the column names in...
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Anonymous posted a comment on discussion Help
What are the column names in your BCF file?
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Hi Avinash, I got the same error, but I have the same in the two files. Created paired...
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Hi, This error indicates that the sample names in the BCF file and the sample names...
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David Stanek posted a comment on discussion Help
Hello, I am trying to run denovogear for trio analysis, I started with three .bam...
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It sounds like you are using a bcf file that is not supported by the dnm module....
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Hi, Sorry for the extremely slow response. Would it be possible for you to provide...
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Hi Tracy, Good question and sorry for the slow response, I should mention that we've...
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Don Conrad posted a comment on discussion Help
Hi Tracy The mapping and base qualities are used by samtools in calculating the genotype...
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I've sent Rena a copy of the updated code, thanks for helping debug this !
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This has been addressed in this pull-request, https://github.com/denovogear/deno...
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Thanks for helping debug Rena, turns out this was a memory issue. DNG upto version...
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Thanks for helping debug Rena, turns out this was a memory issue. DNG upto version...
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Hi Rena, Could you post the full command that you tried ? Also would it be possible...
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Hi Laurent, Sorry for the delay in getting back. Were you able to figure this out...
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Hi Stephen, We do not have a Y specific model yet. But for now one possible strategy...
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Hi Tracy, The denovogear model does look at all possible genotype configurations...
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Hi Tracy, The denovogear model does look at all possible genotype configurations...
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Hi, Would it be possible for you to estimate the mutation rate for your species ?...
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Can you send us a list of the sites that you are calling on the X? In the meantime,...
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It depends on the goals of the analysis. If you have the resources to do this, I...
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The background for this error message is described in the documentation for DNG....
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