Oct 25, 2013 · GATK definitely provides a step by step framework that should get you from raw data to variant calls pretty seamlessly. Remember though that many of their parameters and assumptions are based on their extensive work on human genome projects and may not be necessarily applicable to your bacterial or viral genome project.
The current GATK recommendation for RNA sequencing (RNA-seq) is to perform variant calling from individual samples, with the drawback that only variable positions are reported. Versions 3.0 and above of GATK offer the possibility of calling DNA variants on cohorts of samples using the HaplotypeCaller algorithm in Genomic Variant Call Format ...
Sep 29, 2014 · This short tutorial describes how Variant Call Format encodes data for single nucleotide variants. Every VCF file has three parts in the following order: Meta-information lines (lines beginning with "##"). One header line (line beginning with "#CHROM"). Data lines contain marker and genotype data (one variant per line).
Download Citation | BWAaln-Picard-GATK pipeline for variant calling | Code for BWA mapping of the paired end reads - Picard SAM to BAM conversion - GATK calling of variants in VCF format | Find ...