dkdeconti/DFCI-CCCB-GATK-pipeline

Bash based GATK pipeline to process sequences on the general compute servers

Follow these instructions to run the GATK variant discovery pipeline.

The pipeline is broken into multiple parts.

Part 1 - preprocessing.sh
    * BWA MEM alignment of individual lane fastq
    * RG group annotation
    * Merging of individual lane fastq per sample
    * Deduplication of reads with PicardTools
    * Realignment of indels with GATK
    * Base score quality recalibration with GATK
    * Sequencing depth of coverage QC



#Preprocessing
1. cd to parent directory of project
2. Run prepocessing.sh
preprocessing.sh samples.no_groups.txt samples.lanes probe_ranges.list true
    arg1 = sample list; sample name in first column
    arg2 = sample and lane fastq connection; sample name in first column 
           and a single record of lane fastq
    arg3 = range list for probes in exome seq
           Modify script if using WGS
    arg4 = "true" if paired end
           "false" if single read

# Variant calling