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Developed at Sloan Kettering Cancer Center for use in the Brennan Laboratory. Adapted from Kasthuri Kannan's mutation detection package.

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hxrts/sequencing_pipeline

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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.

About

Developed at Sloan Kettering Cancer Center for use in the Brennan Laboratory. Adapted from Kasthuri Kannan's mutation detection package.

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