If you happen to see a question you know the answer to, please do chime in and help your fellow community members. We encourage our fourm members to be more involved, jump in and help out your fellow researchers with their questions. GATK forum is a community forum and helping each other with using GATK tools and research is the cornerstone of our success as a genomics research community.We appreciate your help!
Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Whole Genome Sequencing data analysis
We are new in whole genome sequencing (WGS) data analysis. Earlier received lots of help and suggestions from GATK team regarding whole exome sequencing analysis and in-house database generation. Recently we are into WGS anaysis and received few raw data from vendor. The Illumina paired end raw data (2 x 150 bp with 30X coverage) was received in parts from 8 lanes (fastq files). I have used FastQC for initial quality checking and have found that in some of the samples the reverse sequences (R2) failed to pass the quality especially at the end. I have attached some of those sample-wise failed fastqc reports here, if you can suggest about the quality of the data and also whether can be used for further analysis using GATK best practices guidelines for SNP & Indel discovery.