Jayoung Kim Ryu

Thanks for extremely fast reply. Sorry - I lost the result while trying to produce the vcfs by using `svaba refilter` without specifying `-o` option. The extracted reads bam is...

I've tried running without `--write-extracted-reads` option which still caused the same problem under 30G memory limit. `bps.txt` file wasn't complete but still is 40Gb.

Hi, thanks a lot for Svaba and all the helpful discussion that's going on here! I'm trying to adopt the codes here to classify SV types and I'm confused whether...

@JaretK @sfrenk Thanks a lot for the helpful scripts! I am a bit confused because the codes provided above still don't seem to agree each other. Is it correct to...

It works! Thanks for the quick fix!

@matthewwardrop I've tried to use the package and the following script works :) `X = Formula('x + z').get_model_matrix(df, output='sparse')`

I had similar error in `workflow.error.log.txt` and my task error log file (`workspace/pyflow.data/logs/pyflow_tasks_stderr_log.txt` says ``` [2020-10-02T18:40:36.040260Z] [compute-e-16-221.o2.rc.hms.harvard.edu] [1281_1] [generateCandidateSV_0000] FATAL_ERROR: 2020-Oct-02 14:40:36 /builder/src/c++/lib/manta/SVCandidateSetData.cpp(125): Throw in function void SVCandidateSetSequenceFragmentSampleGroup::add(const bam_header_info&, const...

It turned out that duplicate reads in bam file (produced by parallel alignment) caused the error. I ended up temporarily editing `src/c++/lib/manta/SVCandidateSetData.cpp` line 151~ so that MANTA won't throw error...

@gbdias Can you see [this page](https://github.com/Illumina/manta/compare/master...jykr:master?diff=split)? The forked repository of altered manta [here](https://github.com/jykr/manta). This code is clumsy but worked for me. You can build manta from the source by following...

I'm getting the same error now for my 6th sample in joint calling with 12 samples (5 250x + 7 30x)- any updates on this issue?