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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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Losing SV calls when merging files #186

Open leonvanmierlo opened 1 year ago

leonvanmierlo commented 1 year ago

Hi,

When I'm using the merge function, I lose some SV calls. I made a Manta- and Delly testfile with each 100 SV calls in them. I merge these files with the function: ./SURVIVOR merge ~/Desktop/sample_files/manta_delly_first100test/sample_files 0 0 0 0 0 0 ~/Desktop/sample_files/manta_delly_first100test/sample_merged_4.vcf (putting everything at 0 so all the SVs are added, if I set a minimum SV length, I expect to lose some calls). I get an output with:

merging entries: 100 merging entries: 100

I expect that the output VCF file has 200 entries but in the output VCF are however only 197 entries.

Why are three SVs not added to VCF file? I think SURVIVOR does some sort of filtering, is that correct? If so, what are the filter settings?

skeremaydin commented 11 months ago

They are on the same line probably if they are close to each other