Genomics - Genomics | Data Science

Annotation of genetic variants

Posted on April 13, 2021 by Ashok Dinasarapu Analysis Genomics Omics

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. >>>

ATAC-seq peak calling with MACS2

Posted on December 5, 2019 by Ashok Dinasarapu Analysis Genomics Omics

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. >>>

Quality control for GWAS studies

Posted on December 16, 2017 by Ashok Dinasarapu Analysis Genomics Omics

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. >>>

Copy number variation discovery workflows using NGS data

Posted on August 19, 2017 by Ashok Dinasarapu Analysis Genomics Omics

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. >>>