ShatterSeek
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parklab
Dear all, we used GATK for CN info and lumpy for SV. The input files are attached. We use LINEAR_COPY_RATIO * 2 as total CN. [genotyped-denoised-copy-ratios-229005560FD.vcf.gz](https://github.com/parklab/ShatterSeek/files/9495128/genotyped-denoised-copy-ratios-229005560FD.vcf.gz) [229005560FD_lumpySV_gt.zip](https://github.com/parklab/ShatterSeek/files/9495141/229005560FD_lumpySV_gt.zip) Here we got...
Hello,  When I ues 20G to post tasks to the server,it still reports errors. Have you ever encountered this problem before? Besides increasing the memory, do you have any...
Hello, I want to use ShatterSeek, and I tried testing it on a sample which seems (based on visual inspection) to have a chromothripsis event on chromosome 3. In the...
Although I have used the code provided by Readme to merge adjacent regions with the same copy number value, it still reported an error in the function "statistical_criteria" that "error...
Hello! I really love this tool and a lot of discussions over here that helped me a lot when analyzing my data. I noticed that in the SV plot generated...
Dear Shatterseek team, I would like to ask if Shatterseek can be used on other references. In principles, all statistical tests seem portable. However, I see that for some criteria...
- works for the processing and the plots - let me know if you need anything else :)
