Simple Nextflow pipeline for a SLURM cluster. $PWD is not used to ensure user views shell scripts.
This workflow will view chr2 from all input files. Merge into single VCF, run vcftools --relatedness2 over the merged file. Outputs a relatedness table: phi > 0.34 is possibly from the same sample. Usage, edit paths to point to own folder:
sbatch ./nextflow_vcf.nf
sbatch ./run_merge.sh
sbatch ./vcftools.sh
This pipeline can be modified to run on the UT HPC to 1) install an Ensembl VEP singularity container. Modifiy paths and uncomment install-vep.sh
Run with sbatch ./install-vep.sh
Modify paths in nextflow_vep.sh to point to a folder containing .VCF files.
Run with sbatch ./nextflow_vep.sh