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GenX relatives detection pipeline

Launcher


docker run --rm --privileged -it -v /media:/media -v /etc/localtime:/etc/localtime:ro grape:latest \
launcher.py find --samples /media/samples.tsv --input /media/input --directory /media/data

Snakemake launch


snakemake --cores all --use-conda -p all

Visualization of the DAG



    snakemake --dag all | dot -Tsvg > dag.svg



snakemake --cores all --use-conda -p all

Force-launch single rule


snakemake --cores all --use-conda -R somerule --until somerule

Simulate data


snakemake --cores all --use-conda -p -s workflows/pedsim/Snakefile

Build snakemake docker container


docker build -t alexgenx/snakemake:latest -f containers/snakemake/Dockerfile -m 4GB .
docker push alexgenx/snakemake:latest

Launch using docker container


snakemake --cores all --use-conda -p --configfile config.yaml --directory /media/data -n

How do I trigger re-runs for rules with updated input files


snakemake -n -R `snakemake --list-input-changes`

Clean-up Snakemake working dir

If you want to use the same working directory for different input files it is better to clean-up it first


snakemake --delete-all-outputs --cores 1

References

  1. For lifting: chain = '/media/ref/hg38ToHg19.over.chain.gz' ref = '/media/ref/human_g1k_v37.fasta', size = 3G
  2. For phasing: map = '/media/ref/tables/genetic_map_hg19_withX.txt.gz', size = 51M bcf = '/media/ref/1000genome/bcf/1000genome_chr{1..22}.bcf', size = 14G
  3. For imputation: m3vcf = '/media/ref/Minimac/{1..22}.1000g.Phase3.v5.With.Parameter.Estimates.m3vcf.gz', size = 3.2G
  4. For interpolation: map = '/media/ref/genetic_map_b37/genetic_map_chr{1..22}_combined_b37.txt', size = 120M
  5. For imputation check: tab = '/media/ref/1000genome/allele_info/ALL.wgs.phase3_shapeit2_mvncall_integrated_v5b.20130502.sites.only_rs.biallelic.tab', size = 12G