LOCAL INSTALL PROCEDURE:
MAKE SURE YOU HAVE SET GIT TO ONLY UPDATE CURRENT BRANCH git config global push.default=current
in project directory: git init git remote add origin master git@github.com:scholzmb/GATKBacteria.git git pull git branch git checkout
proceed.
else (others) clone, or branch, and make pull requests.
This repository contains all code needed to generate a SNP analysis from bacterial samples. It is designed to work with multiple samples at a time.
Scripts must be edited to use:
- GATK formatted reference (REF=)
- Genbank formatted annotation (GBK=)
- VCF file of known snps (Blank.vcf is provided if no dbsnp is available) (KNOWN=)
tools are hard-coded with paths to use GATK, TRAMS, and PICARDtools vcf2trams.pl is a custom perl script used to split multi-g.vcf files (with >1 sample) from GATK into trams compatible files. it can be found in contrib/
Samples must be trimmed and aligned to reference prior to running GATK. standard protocol is
trimmomatic + FastQC
bwa mem