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High throughput genomic sequencing pipeline

Installation

When cloning this repo for the first time you must install the necessary tools.

  1. Create a 'tools' directory in the root folder
  2. Place a copy of annovar, samtools, etc.

Executing the script

production run: python call-mutations-indels.py -s sample_info.txt -p path_file.sh -d outputdir [-b intervals.maf]

debug run: python -i call-mutations-indels.py -s sample_info.txt -p path_file.sh -d outputdir [-b intervals.maf]

This pipeline is currently installed on the hopp-cli server and must be executed from /home/sam/HOPP-Informatics/projects/sequencingPipeline.

Build reference index (if adding new assembly)

Generate the BWA index bwa index -a bwtsw reference.fa

Generate the fasta file index samtools faidx reference.fa

Generate the sequence dictionary java -jar picard.jar /home/sam/tools/picard-tools-1.130/CreateSequenceDictionary REFERENCE=reference.fa OUTPUT=reference.dict

Warning

This pipeline is still in development and produces known errors use at your own risk.