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Not able to merge insertions #199
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I have the same problem |
Hey there, Btw. I would suggest this: (10k is a bit big) The strand information might also be causing the issue... Thanks |
Hello, I did not find this conversion script |
I have the same problem. @beantkapoor786 Have you solved the problem? If so, please share the method. Thank you! |
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. |
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
andSVLEN=1
? Please provide your thoughts. I am using the following command to do the merge but output vcf file is empty.Output message -
I have also attached the insertion vcf files here in case you want to look at them. Thanks!
insertions.zip
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