PopDel identifies medium-size deletions jointly in tens of thousands of genomes - Variant call sets

This data set contains the variant calls sets generated by different tools for the benchmarks in the paper PopDel identifies medium-size deletions simultaneously in tens of thousands of genomes. It includes the VCFs/BCFs for the following test cases:

Random deletion simulation on up to 1000 chromosome 21 samples

1000 Genomes Project deletions inserted into simulated chromosomes 17 to 22 of up to 500 samples

HG001 (NA12878)

Trio of HG002 + HG003 + HG004

Polaris Diversity cohort

Polaris Kids cohort

Further, the long and short read reference call sets for HG001 are provided. For HG002 the reference call set and the high confidence regions by the Genome in a Bottle consortium are provided.

For details on how the files have been created, please refer to the paper and the script repository on GitHub.