Difference between Delly merge and bcftools merge - Germline SV Calling

[Travis Williams]

Dear Tobias,

I am currently performing the germline SV calling pipeline on approximately 90 different deep coverage samples.  I noticed that in the beginning of your pipeline you use delly merge to create a unified sites list.bcf file, but the second to the last step uses bcftools merge.

Can you help clarify why you would use the delly merge over the bcftools merge? Thank you.

[Tobias Rausch]

Hi,

bcftools merge creates a multi-sample VCF from non-overlapping sample sets. It does not change the SV sites. Delly merge creates a site list and not a multi-sample VCF. delly merge deals with merging redundant SV sites and selecting the best representative SV for a cluster of SVs.

Best, Tobias

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