Jeremiah Wala

I see you found issue #29 which describes why this is more difficult / less-well-defined for SVs than for SNVs. It's a good question. I would suggest that the best...

You have to have the genome fasta indexed with both bwa and samtools faidx. I’d run or rerun those on the genomes and try again. > On Oct 15, 2021,...

I think what’s happening is that it’s getting a memory load when reading back in the huge bps.txt file to convert to VCF. Can you confirm that it completed the...

This is very odd, svaba should be much more judicious with memory. Is this with multi-thread or single thread? Any other tips you could give (e.g. the run command) so...

Hi Catherine, Hmm, this is odd. Would you be able to email me ([email protected]) a Dropbox link with the reference genomes and indicies? I want to try and recreate so...

Hi Catherine, I'm still not able to recreate this error. I indexed hg38 and it loads well. Are you also indexing with "samtools faidx"? Best, Jeremiah

Ah-ha! Thank you for solving this issue @Hansol-Park and @nukaemon. I'm leaving this open as a reminder to patch this so that either naming convention can work.

Hmm, that's strange I've not heard of that before. You're right that when multi-threaded, svaba will do different genomic windows in non-deterministic order because the threads will just grab them...

If it's not protected data (usually it is), then I could try to take a look, finally getting some open time to work on this stuff. However, I doubt, but...

Thanks for bumping this and for your patience. Can you check the *.bps.txt.gz file to see if the SV called in sample 1 is listed for the other two? *.bps.txt.gz...