Structural Variant Catalog

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).

Re-genotyping of SVs

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

SV properties

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.