ShatterSeek

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Problems about the CN & SV input.

1

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...

mistClaud

Cannot allocate memory

1

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...

lilili123lj

Only interchromosomal SVs used for chr_breakpoint_enrichment and pval_exp_chr ?

4

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...

e-sollier

Error in statistical_criteria

3

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...

chengwenxuan1997

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...

lichennan123

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...

fabrimafe

- works for the processing and the plots - let me know if you need anything else :)

soymintc