The missing indels: an estimate of indel variation in a human genome and analysis of factors that impede detection.

ABSTRACT: With the development of High-Throughput Sequencing (HTS) thousands of human genomes have now been sequenced. Whenever different studies analyze the same genome they usually agree on the amount of single-nucleotide polymorphisms, but differ dramatically on the number of insertion and deletion variants (indels). Furthermore, there is evidence that indels are often severely under-reported. In this manuscript we derive the total number of indel variants in a human genome by combining data from different sequencing technologies, while assessing the indel detection accuracy. Our estimate of approximately 1 million indels in a Yoruban genome is much higher than the results reported in several recent HTS studies. We identify two key sources of difficulties in indel detection: the insufficient cove

SUBMITTER: Jiang Y 

PROVIDER: S-EPMC4551921 | biostudies-literature | 2015 Sep

REPOSITORIES: biostudies-literature