DNA-seq

Analysis of Whole Exome (or Whole Genome) DNA-seq data to call germline and somatic variants from individual samples (not paired tumor-normal samples) using GATK (4.1.8.1) pipelines

• HaplotypeCaller pipeline for germline variants

• Mutect2 pipeline for somatic variants

Reference genome and variant data can be downloaded from GATK

GATK resource bundle

Download Google Cloud bucket of general hg38 resources

• gsutil cp gs://genomics-public-data/resources/broad/hg38/v0 path-local-folder

Download Google Cloud bucket of hg38 resources for Mutect2 somatic variant caller

• gsutil cp gs://gatk-best-practices/somatic-hg38 path-local-folder

Contact

Ting Wang ([email protected]).