Moritz Smolka

Hi Mike, currently Sniffles2 supports VCF & VCF.gz output only - I just added BEDPE output to the planned features list. Before this is implement, using a VCF->BEDPE conversion tool...

Hi Marc, sorry for the delayed response - may I ask what kind of minimum support value you were using with Sniffles1 and what level of read support those inversions...

Hello, this may be caused by deletions being split up within an alignment across highly repetitive regions. We recommend running Sniffles2 with a tandem repeat annotations .bed file (which can...

Sniffles uses different clustering parameters in the repeat regions to account for SVs being split up into multiple smaller events by read aligners - so yes, even though you are...

Hello again! it seems from your results that your region may not benefit from this mode, which is designed to handle simple repeats, as you noted. In some cases such...

Sounds like your region also leads to disagreement between mappers in terms of how they split up read alignments - this can happen in regions containing complex / fragmented SVs....

Hi ErminZ, Genotyping is currently only supported for diploid genomes, but detecting SVs in a viral sample with Sniffles would not be a problem (without changing --genotype-ploidy) - however the...

Hi again Ermin, It sounds like possibly some of the read alignments may not be passing Sniffles2 preprocessing filter. This could be the case if a larger fraction of your...

Hi ErminZ, thanks for your reply - what would be worth a try is to use the `--min-alignment-length` and `--mapq` parameters (these should work fine) together with the `--no-qc` option...

Hi again ErminZ and sorry for the late reply, of course I can take a look at the files to see if theres a hint as to what exactly is...