1000 Genomes Project SV: Phase 3 - GooglingTheCancerGenome/sv-channels GitHub Wiki

High coverage samples:

sample	coverage	insert size median	insert size sd
HG00096
HG00268
HG00419
HG00759
HG01051
HG01112
HG01500
HG01565
HG01583
HG01595
HG01879
HG02568
HG02922
HG03006
HG03052
HG03642
HG03742
NA12878
NA12891
NA12892
NA18525
NA18939
NA19017
NA19238
NA19239
NA19240
NA19625
NA19648
NA20502
NA20845

Processing the 1KG dataset with sv-callers:

cd /project/gcg/Data/1KG
git clone https://github.com/GooglingTheCancerGenome/sv-callers.git
cd sv-callers

snakemake --use-conda --latency-wait 30 --jobs 30 \
--cluster 'xenon scheduler slurm --location local:// submit --name smk.{rule} --inherit-env --cores-per-task {threads} --max-run-time 7500 --max-memory {resources.mem_mb} --working-directory . --stderr stderr-%j.log --stdout stdout-%j.log' &>smk.log&