about somatic SV calling

[dongjuleem]

Sorry for the basic question. I am currently conducting somatic SV calling using WGS paired data from 30 tumors and controls. I have used the pipeline to call each paired data as follows:

delly call -x hg19.excl -o t1.bcf -g hg19.fa tumor1.bam control1.bam
delly filter -f somatic -o t1.pre.bcf -s samples.tsv t1.bcf

As a first question, I noticed that some candidates with filter=pass in delly call disappear after the delly filter process.
I would like to inquire about the reason for this and whether this process is correct.

As a final question, in the README, it recommends the following step:
delly call -g hg19.fa -v t1.pre.bcf -o geno.bcf -x hg19.excl tumor1.bam control1.bam ... controlN.bam

Does this mean I have to repeat this process 30 times for each of the 30 WGS paired data?"

always thanks