Low coverage massively parallel genome sequencing for non-invasive prenatal testing (NIPT) of common aneuploidies is one of the most rapidly adopted relatively low-cost DNA tests. Since aggregation of reads from a large amount of samples allows to overcome problems of extremely low coverage of individual samples, the possible reuse of the data generated during NIPT testing for genome scale population specific frequency determination of single nucleotide variants is described.
We utilized sequenced reads from 1548 individuals (low coverage ~0.2x) to estimate common genomic variation in Slovak population. SNP, insertion and deletion variants are available in form of VCF file. Detailed description of data preparation, processing and results would be available after paper submission.