search

fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
337 stars 46 forks source link

Not able to merge insertions #199

Open beantkapoor786 opened 11 months ago

beantkapoor786 commented 11 months ago

Hello Fritz,

We have a tree genome pedigree in which we are comparing 5 different genomes to the reference genome. We aligned each genome using mummer4 and called structural variants. Now, we want to merge those structural variants using SURVIVOR's merge function. We were able to merge deletions and inversions but cannot merge insertions. Is it because the start and end positions in insertions are in the format END=START+1 and SVLEN=1? Please provide your thoughts. I am using the following command to do the merge but output vcf file is empty.

SURVIVOR merge insertions.txt 10000 1 1 1 0 1 mummer_insertions_merged.vcf

Output message -

merging entries: 51273
merging entries: 79656
merging entries: 75335
merging entries: 77095
merging entries: 79632

I have also attached the insertion vcf files here in case you want to look at them. Thanks! insertions.zip

sd880131 commented 8 months ago

I have the same problem

fritzsedlazeck commented 8 months ago

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 ?

Btw. I would suggest this: (10k is a bit big) SURVIVOR merge insertions.txt 10000 1 1 0 0 1 mummer_insertions_merged.vcf

The strand information might also be causing the issue...

Thanks Fritz

JiaB-He commented 7 months ago

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 ?

Btw. I would suggest this: (10k is a bit big) SURVIVOR merge insertions.txt 10000 1 1 0 0 1 mummer_insertions_merged.vcf

The strand information might also be causing the issue...

Thanks Fritz

Hello, I did not find this conversion script

zhiyongli1995 commented 4 months ago

I have the same problem. @beantkapoor786 Have you solved the problem? If so, please share the method. Thank you!

beantkapoor786 commented 3 months ago

Hello, apologies for the late response. I couldn't do it using survivor but found another tool to merge the SVs - https://github.com/DecodeGenetics/svimmer

Hope this helps.