Annotation of genetic variants

Tools such as ANNOVAR, Variant Effect Predictor (VEP) or SnpEff annotate genetic variants (SNPs, INDELS, CNVs etc) present in VCF file. These tools integrate the annotations within the INFO column of the original VCF file. >>>
read more

ATAC-seq peak calling with MACS2

ATAC-seq (Assay for Transposase Accessible Chromatin with high-throughput Sequencing) is a next-generation sequencing approach for the analysis of open chromatin regions to assess the genome-wise chromatin accessibility. >>>
read more

Quality control for GWAS studies

An important step in the analysis of genome-wide association studies (GWAS) is to identify problematic subjects and markers. Quality control (QC) in GWAS removes markers and individuals, and greatly increases the accuracy of findings. >>>
read more

Copy number variation discovery workflows using NGS data

Copy number variations (CNVs) represent gain or loss of genomic regions. CNVs transmit from parents to offspring or arise de novo and play important role in neuro-psychiatric disorders and cancers. >>>
read more