Run Delly to get structural variants
March 31, 2023
Installation
Using docker image which pulls the latest version (v1.1.6) by default.[1]
docker pull dellytools/delly
Installation for Delly (v0.7.8)
wget https://github.com/dellytools/delly/releases/download/v0.7.8/delly_v0.7.8_linux_x86_64bit
chmod +x delly_v0.7.8_linux_x86_64bit
Usage
Input file
Delly needs a sorted, indexed and duplicate marked bam file for every input sample. [2]
delly call -g hg19.fa input.bam > delly.vcf
delly call [OPTIONS] -g <ref.fa> <sample1.sort.bam> <sample2.sort.bam>
Somatic SV calling
- At least one tumor sample and a matched control sample are required for SV discovery
delly call -x hg19.excl -o t1.bcf -g hg19.fa tumor1.bam control1.bam
Important check
To avoid the error "Normal sample not speficied below" Try
bcftools query -l t1.bcf
You should see a pair:
tumor_name control_name
- Somatic pre-filtering requires a tab-delimited sample description file where the first column is the sample id (as in the VCF/BCF file) and the second column is either tumor or control.
delly filter -f somatic -o t1.pre.bcf -s samples.tsv t1.bcf
What is inside `samples.tsv`?
tumor_name tumor
control_name control
- Genotype pre-filtered somatic sites across a larger panel of control samples to efficiently filter false postives and germline SVs. For performance reasons, this can be run in parallel for each sample of the control panel and you may want to combine multiple pre-filtered somatic site lists from multiple tumor samples.
delly call -g hg19.fa -v t1.pre.bcf -o geno.bcf -x hg19.excl tumor1.bam control1.bam ... controlN.bam
- Post-filter for somatic SVs using all control samples.
delly filter -f somatic -o t1.somatic.bcf -s samples.tsv geno.bcf