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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering

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error merging vcfs

msubirana opened this issue · comments

commented

Hi,

I am trying to merge 4 vcfs from 4 different callers in the same samples (Gridss, manta and lumpy and delly) but the same samples for different callers are not merging in the same sample and instead survivor is creating different columns with the same sample name but adding _1, _2 and _3.

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  NET51_TI
        NET51_TI_1      NET51_TI_2      NET51_TI_3      NET52_TI        NET52_TI_1      NET52_TI_2      NET52_TI_3

When I expect only one NET51_TI for example merging the same SV for the different variants and appending the others in the same sample. Any suggestions?