breakseq2
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bioinform
BreakSeq2: Ultrafast and accurate nucleotide-resolution analysis of structural variants
Or maybe how to convert a breakpoint library from other hg to hg 38?
Dear Breakseq2 developers, I am trying to run the software through SVE (https://github.com/TheJacksonLaboratory/SVE) wrapper on a BAM file obtained aligning sequence reads to hg38 reference (with alternative haplotypes). However, I...
Greetings. All pip install attempts from your "2.2.tar.gz" fail. Error "SyntaxError: Missing parentheses in call to 'print'. Did you mean print(version)?" Do you have any leads? Environment is Centos 7.6....
I would like to use `BreakSeq2` but am unsure of how to create a breakpoint library for other model organisms; specifically _C. elegans_. It's [unclear from the documentation](http://bioinform.github.io/breakseq2/) how a...
The error message shows can't find 1.fa in my outputdir. but I did not find anything wrong in install and script. `INFO 2019-11-01 09:32:46,750 /home/bpvast/01.test/1031_SV_test/breakseq2-2.2/scripts/run_breakseq2.py Command-line: /home/bpvast/01.test/1031_SV_test/breakseq2-2.2/scripts/run_breakseq2.py --reference /home/bpvast/01.test/1031_SV_test/breakseq_sv --bams...
Hi, I am trying breakseq2 in tomato genome. if breakseq2 only work for human genome ? If you have any method to generate breakpoint library? thanks a lot, Kai
The VCF output file appears to contain 0-based coordinates. As per the specification, VCF files should contain 1-based coordinates (https://samtools.github.io/hts-specs/VCFv4.1.pdf). (FYI: VCF also specify that "telomeres are indicated by using...
