Losing SV calls when merging files

[leonvanmierlo]

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]

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