Problems about the CN & SV input.

[mistClaud]

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
229005560FD_lumpySV_gt.zip
Here we got some confusion:

1. We wonder if the CN info must be continuous because there are gaps between each segment in our data.
2. Are the SVs strictly accurate and filtered, or can they be kind of loose?
3. We can not get the interleaved SVs in 60 samples. Is there any potential reason or suggestion to solve this? Actually, we did not understand how interleaved SVs formed.
4. Is looking by eyes the only way to tell interleaved SVs?
5. Here is the criteria we used to judge the chromothripsis. Is it feasible?
   (1) Osillating CN >= 7.
   (2) Pval chr breakpoint enrichment < 0.05 | Pval exp breakpoints < 0.05.
   (3) Pval fragment joins >0.05.
   (4) Interleaved SVs >= 6.

[mistClaud]

229005560FD.zip
Here are the results we got.