Fritz Sedlazeck

Hey there, mmh the SVLen =1 is an issue. I wrote that wrapper script a while back for something... are you using this converter script from SURVIVOR for mummer ?...

yes

Thanks. Yeah survivor is really only for structural variants.. so no on snv. There are multiple tools for snv merging/comparison. The easiest might be bcftools.

Mmh thats not good. Please check the parameters for sure... Can you post the command? Thanks Fritz

so on a per sample bases you can get the ALT coloumn completelfy filled with providing the reference fasta. You are probably asking for the merge (across different samples)? This...

So start is the left most and stop is the right most position/breakpoint. The positions are defined by the read alignments (ie. based on the split or alignment signal) there...

Oh I see my reply was on a per read/sample level. You are interested in the population/ across sample merge. So again the start is always the left most and...

I am closing this. Hope its answered.

Dear @ymcki we are just releasing a new version. The code version is now alreayd online for a few days. This should improve the behavior to not over merge INS...

Sorry no. so that file is just so the merge of SV candidates (internally) are more relaxed in tandem repeat regions. Tandem repeat are not duplications! Sniffles reports duplciations independent...