A repository for human genetic structural variants (SVs) discovered by Delly in the 1000 Genomes cohort of samples. SV sites are provided for deletions (DEL), insertions (INS) and duplications (DUP).
To re-genotype these SVs with Delly in a different cohort of samples (e.g., the YRI trio):
./delly -t DEL -g hg19.fa -v DEL.hg19.vcf.gz -o DEL.regeno.bcf NA19238.bam NA19239.bam NA19240.bam
The genotyping can be run in parallel, using BCFtools to merge the BCFs/VCFs:
./delly -t DEL -g hg19.fa -v DEL.hg19.vcf.gz -o DEL.NA19238.bcf NA19238.bam
./delly -t DEL -g hg19.fa -v DEL.hg19.vcf.gz -o DEL.NA19239.bcf NA19239.bam
./delly -t DEL -g hg19.fa -v DEL.hg19.vcf.gz -o DEL.NA19240.bcf NA19240.bam
./bcftools merge -o DEL.regeno.bcf -O z DEL.NA19238.bcf DEL.NA19239.bcf DEL.NA19240.bcf
Visualizing the SV size and frequency spectrum using svprops:
./svprops INS.hg19.vcf.gz > INS.tsv
Rscript svprops/R/svprops.R INS.tsv
To visualize multiple SV types in the same plot:
cat DEL.tsv DUP.tsv INS.tsv | sort -r | uniq > All.tsv
Rscript ~/scripts/cpp/svprops/R/svprops.R All.tsv
An example plot is shown here.