Supporting data for "Fast and accurate relatedness estimation from high throughput sequencing data in the presence of inbreeding"

The estimation of relatedness between pairs of possibly inbred individuals from high-throughput sequencing (HTS) data has previously not been possible for samples where we can not obtain reliable genotype calls, as in the case low coverage data. We introduce ngsRelateV2, a major revision of ngsRelateV1, a program which originally allowed for estimation of relatedness from HTS data among non-inbred individuals only. The new revised version takes into account the possibility of individuals being inbred by estimating the nine condensed Jacquard coe cients along with various other relatedness statistics. The program is threaded and scales linearly with the number of cores allocated to the process. The program is available as an open source C/C++ program under the GPL license and hosted at https://github.com/ANGSD/ngsRelate. To facilitate easy analysis, the program is able to work directly on the most commonly used container formats for raw sequence (BAM/CRAM) and summary data (VCF/BCF).