github官网：https://github.com/dellytools/delly
hg38.excl 下载：https://github.com/dellytools/delly/tree/1ac07d0420e8a111076949ac8aab6361eb625e60/excludeTemplates
Germline short-read SV calling
# SV calling is done by sample for high-coverage genomes or in small batches for low-coverage genomes
delly call -g hg38.fa -o s1.bcf -x hg38.excl sample1.bam
# Merge SV sites into a unified site list
delly merge -o sites.bcf s1.bcf s2.bcf ... sN.bcf
# Genotype this merged SV site list across all samples. This can be run in parallel for each sample.
delly call -g hg38.fa -v sites.bcf -o s1.geno.bcf -x hg38.excl s1.bam
delly call -g hg38.fa -v sites.bcf -o sN.geno.bcf -x hg38.excl sN.bam
# Merge all genotyped samples to get a single VCF/BCF using bcftools merge
bcftools merge -m id -O b -o merged.bcf s1.geno.bcf s2.geno.bcf ... sN.geno.bcf
# Apply the germline SV filter which requires at least 20 unrelated samples
delly filter -f germline -o germline.bcf merged.bcf
# 构建批量运行代码
cnv calling
delly cnv -g example/ref.fa -m example/map.fa.gz -c out.cov.gz -o cnv.bcf example/sr.bam