How ca I merged same samples called by different tools without duplicating IDs?

[itsmestewart]

Hello there,

i have 400 samples, i have called SVs using manta and Smoove, i now want to merge them using SURVISOR. These the out of SVs variants have the same sample ID the difference is only the tools used to call variants.

I tried merging with SURVIROR, it was successful, only that there sample ID duplicates, eg SV variants from MAnta writen as Sample1, Sample1_1, and those from smoove as sample2,sample2_1 in a merged vcf.

Before merging, I splited manta and lumpy vcf per samples.

How can i siccessufl merged the SVs without duplicating sample ID in merged vcf?

Does duplicated sample ID affect SVs counts?

Thank you for assistace and patient for my basic questions

[kunmonster]

Hava u solved this problem?