BWA, GATK and snpEff + GE (human (hs37d5) only, for small amplicon data, PE) [IN: fastq (paired-end) (max 10)]
This pipeline aligns short reads from NGS to a reference genome with BWA at first and visualize them by our genome browser, GenomeExplorer(GE) on the web.Then it calls genomic variants with GATK. Finally called variants including SNVs and short InDels are annotated by snpEff program which predicts influence level of amino acid changes.You can add annotations including SNP frequency made by this project from public archives. Supported organism of this pipeline is only human. Compared with Exome pipeline, Picard Markduplicates and some GATK recalibration were removed.