Basic BASH pipeline for calling rare germline SNVs from FASTQ files using GATK
Bioinformatic pipeline to align reads from NextGen sequencing FASTQ files (demultiplexed reads) using BWA to call rare germline single nucleotide variants (SNVs) using GATK.
This pipeline can be altered to call small insertion-deletions (indels), as mentioned in the comments. The alignment step assumes reads are paired-end and longer than 75 bps. Review commented commands for alternative parameters and tools if either condition is unmet.
Post variant calling filtering based on functional annotations are mentioned in comments and two examples performed by the script.