Bioinformatics Data Analysis Pipeline- Genetic Variant Analysis

GATK

Genome Analysis Toolkit Best Practices Pipeline
Reference: PMID: 25431634
Contact: Qin Ma
VarScan

Tool for detecting SNPs,indels, somatic mutations and copy number variants in exome data.
Reference: PMID: 22300766
Contact: Qin Ma
HaplotypeCaller

Tool under GATK to call germline SNPs and indels via local re-assembly of haplotypes.
Reference: https://www.biorxiv.org/content/10.1101/201178v3
Contact: Qin Ma
Mutect

Tool under GATK to call somatic SNVs and indels via local assembly of haplotypes.
Reference: PMID: 20644199
Contact: Qin Ma
CNVKit

Genome wide copy number detection and visualization from targeted DNA sequencing.
Reference: PMID: 27100738
Contact: Qin Ma
VEP

Variant Effect Predictor to annotate variants using Ensembl.
Reference: PMID: 27268795
Contact: Qin Ma
VCFtools

A package designed to access methods to manage complex genetic variation in form of vcf format.
Reference: PMID: 21653522
Contact: Qin Ma
Picard

A set of command line tools for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.
Reference: https://broadinstitute.github.io/picard/
Contact: Qin Ma