ZAMS: A Pipeline for Accurate Variant Calling by Integrating Various Tools

Masum Billah
2019 Figshare  
Meaningful analysis of next-generation sequencing (NGS) data, extensively produced by genomics studies, relies largely on the accuracy and consistency of the genome variants and genotypes. Hence, a systematic comparison of the variant callers could give crucial outputs in any NGS-based genomics experiment. Although several tools are available for variant calling, accuracy of these tools and their interpretation in different perspectives are not fully reliable. Therefore, A systematic comparison
more » ... of the variant callers could provide important outcomes in any structural genomics experiment. The assessment of several commonly used tools has also shown that a single tool cannot meet all these requirements. Additional experiments and extensive manual work are required to identify false positive and false negative variants. To overcome the situation we devised a smart combination and output filtration by using available open source pipeline. We proposed a ZAMS pipeline, which is an automatic pipeline for calling single nucleotide polymorphisms and short indels, using a new artefact and polymorphism score and combining and filtering the output of three open source variant calling pipeline. This pipeline reduces false positive as well as false negative variants through a combination of these three tools output results.
doi:10.6084/m9.figshare.7991618 fatcat:oodp7d3nevfpneyxb5c2gj6swe