leone93

Results 17 comments of leone93

How much memory does minimap2 requires?

I have the same problem. Is it possible to limit the memory usage of minimap2?

fastp trim polyG is not working when the data is large

yeah, also for me is not working (version 0.23.4)

Expected DR field

For what I saw survivor need the AD field to be separated in 2 value separated by ":" to be recognized, like DR:DV. He cannot understand the comma separated value

INV, DEL, DUP with huge SVLENs in sniffles 2.0.7

Same problem here. Did you find a solution to filter these events @ddrichel ( @fritzsedlazeck )? Otherwise, it isn't easy to use this tool, especially going to the multisample level....

INV, DEL, DUP with huge SVLENs in sniffles 2.0.7

That was honestly my only idea to solve this problem. Which SVLEN did you use? Thanks, Dmitriy

INV, DEL, DUP with huge SVLENs in sniffles 2.0.7

I will give it a look. Thank you! (however I was thinking to choose a conservative threshold)

vcfwave 1.0.9 terminates after throwing an instance of 'std::out_of_range'

> > I also got the same error. Does anyone have any solutions? > > It seems that the absence of certain annotations in the INFO column, such as AF...

merging different SV type?

I'm trying to build a parser to simplify the SURVIVOR output in order to make it more similar to the one from bcftools (and your actual example). the problem of...

<INS> sequence missing in ALT field and represented as C<INS>, T<INS>, A<INS>, G<INS>

Hi @hermannromanek and @fritzsedlazeck ! Sorry for the late response! here you are a couple of these INS lines from a single sample vcf: ```Chr1 41126819 Sniffles2.INS.4E8S0 T T 60...

vg giraffe runs unusually slowly on Illumina paired-end reads on one user's system

@adamnovak @upsm-123 I find the same problem. I tried the last three versions of VG (from 1.66 to 1.68) to be sure it's not related to this, but I see...