Methods and processes for non-invasive assessment of genetic variations

A system comprising one or more processors and memory, which memory comprises instructions executable by the one or more processors, and which instructions executable by the one or more processors are configured to:

• (a) access sequence reads of cell-free nucleic acid from a test sample from a pregnant female bearing a fetus;
• (b) map the sequence reads to genomic sections of a reference genome;
• (c) access a subset of the genomic sections selected according to a fragment length ratio X/Y obtained for the test sample or a group of samples for each genomic section, wherein X is the sum of reads that map to the genomic section and are from nucleic acid fragments that are shorter than a first selected fragment length, and Y is the sum of reads that map to the genomic section and are from nucleic acid fragments that are shorter than a second selected fragment length;
• and
• (d) identify the presence or absence of a fetal copy number variation according to an amount of sequence reads mapped to the subset of genomic sections.