Performance assessment of variant calling pipelines using human whole exome sequencing and simulated data.

ABSTRACT:

Background

Whole exome sequencing (WES) is a cost-effective method that identifies clinical variants but it demands accurate variant caller tools. Currently available tools have variable accuracy in predicting specific clinical variants. But it may be possible to find the best combination of aligner-variant caller tools for detecting accurate single nucleotide variants (SNVs) and small insertion and deletion (InDels) separately. Moreover, many important aspects of InDel detection are overlooked while comparing the performance of tools, particularly its base pair length.

Results

We assessed the performance of variant calling pipelines using the combinations of four variant callers and five aligners on human NA12878 and simulated exome data. We used high confidence variant cal

SUBMITTER: Kumaran M 

PROVIDER: S-EPMC6580603 | biostudies-literature | 2019 Jun

REPOSITORIES: biostudies-literature