Performs genotyping, diplotype identification, phenoptying, and reporting
From the src directory:
python3 -m venv env
source env/bin/activate
python3 -m pip install -r requirements.txt
lmPGX requires the following:
- python3
- GATK4 (tested with GATK4.0.3.0)
- dbsnp VCF file
- java (tested with 1.8.0
- picard (tested with 2.18.3 Update the paths to these tools/resources in lib/config.yml, as well as the other paths specified by lib/config.yml (reference FASTA file and GATK temp out directory). It's best to update all paths in lib/config.yml to be absolute paths
- activate Python venv source env/bin/activate
python3 src/pgx.py -b BAM/CRAM -s SAMPLE_ID -o OUTDIR -c lib/config.yml
#Alternatively, the pipeline can accept a VCF instead of bam. Note though that this has been tested less thoroughly, and the VCF must look like the allbases VCF produced by the variant calling portion of lmPGX
python3 src/pgx.py -v VCF -s SAMPLE_ID -o OUTDIR -c lib/config.yml