Somatic SV calling in 50 matched tumor-normal sample

[Min Hui Tan]

Hi everyone,

I am looking to discover somatic SV in 50 breast cancer samples (each with a corresponding normal).

I am trying to follow the Somatic Calling steps, and I'd like to check that i should run each step 50 times (especially step 3.1) - is that right?

Step 1: SV Discovery (run for each sample/ tumor-normal pair)

delly call -o t1.dis.bcf -g hg38.fa 1T.sorted.bam 1N.sorted.bam

Step 2: Somatic pre-filtering (run for each sample)

delly filter -f somatic -o t1.pre.bcf -s sample1.tsv t1.dis.bcf

where i'll generate sample1.tsv 50 times (for each sample/ run ) as such

1T.sorted    tumor

1N.sorted   normal

Step 3.0: Generate panel of normal - by combining t*.pre.bcf of all 50 samples (run this once)

delly merge t1.pre.bcf t2.pre.bcf ..... t50.pre.bcf -o merged.pre.bcf

Step 3.1: Genotyping (run for each sample)

delly call -g hg38.fa -v merged.pre.bcf -o genotype.bcf 1T.sorted.bam 1N.sorted.bam 2N.sorted.bam..... 50N.sorted.bam

Step 4: Post filtering

delly filter -f somatic -o t1.somatic,bcf -s sample1.tsv genoptye.bcf

Does the steps look right?

OR - is there a way to run step 3.1 only once? OR perhaps run step 3.1 50 times, then merge the genotype.bcf from each run into merged.genotype.bcf for step 4.

Thank you in advance for your time - as I don't fully understand the steps

Many thanks,

Min