Check-up prior to indexing possibly missing about shatterseek HOT 4 CLOSED

Hi @vladimirtomic ,
I recently meet the problem too, could you please give me any idea about fix it?
Thans for your help.
Best.
Zhang

from shatterseek.

Hi @zhang919,

I've tried to find if and how I've fixed it, but couldn't find it. We probably skipped the processing of that sample.

Best,
Vladimir

from shatterseek.

Hi @vladimirtomic,
Thanks for your kindly reply, I found that it can run well in hg38 coordinate system, but it can't run on hg19 converted by liftOver, which is very interesting. All in all this may harmless. Could you allow me to follow up a question, I notice the section "Recommended cut-off values" tell:

High confidence: at least 6 interleaved intrachromosomal SVs, 7 contiguous segments oscil-
lating between 2 CN states, the fragment joins test, and either the chromosomal enrichment
or the exponential distribution of breakpoints test.
High confidence: at least 3 interleaved intrachromosomal SVs and 4 or more interchromosomal
SVs, 7 contiguous segments oscillating between 2 CN states and the fragment joins test.
Low confidence: at least 6 interleaved intrachromosomal SVs, 4, 5 or 6 adjacent segments os-
cillating between 2 CN states, the fragment joins test, and either the chromosomal enrichment
or the exponential distribution of breakpoints test.

I noticed pval_fragment_joins and inter_pval_fragment_joins in the result, I am not sure that it is appropriate to adopt whats one. Could you please give me some suggestions?
Thanks for your reading and help again.
Best.
Zhang

from shatterseek.

Hi @zhang919, I'd like to help, but I've used ShatterSeek almost two years ago and don't remember any of the details.

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