NOTES
Installation
singularity pull -F library://hmgu-itg/default/burden_testing:latest
singularity inspect burden_testing_latest.sif
singularity exec burden_testing_latest.sif help
singularity exec burden_testing_latest.sif single_cohort_munge_variantlist -h
singularity exec burden_testing_latest.sif prepare-regions -h
singularity exec burden_testing_latest.sif make-group-file -h
singularity exec --containall burden_testing_latest.sif step2 --help
for the latest or :1.5.4
, see wiki instructions on installation, data and SMMAT.
Debugging
Additional information can be obtained with singularity exec --help
. For debugging, e.g., on VCF2GDS, one can invoke the singularity shell via
singularity shell --bind ${PWD} --containall --shell /usr/bin/bash burden_testing_latest.sif
and the container has its own HOME directory within which ~
is recognised.
- The embedded call to
sbatch
implicates the--wait
option as the succeeding steps would require its full results. - The array jobs could be altered to accommodate software and model (BOLT-LMM, GCTA
--fastGWA/fastGWAS-lr
for mixed model/linear regression). - The group filess for rare variant analysis have been provided by the central analysis team. Note that (a). They are whole-genome so are preferably split by chromosome. (b). No groupings are contained for chromosomes X and Y, so they could be dropped from the analysis.
File upload
This is a heavy burden for the system, so the files are compressed first with sftp.sb
.
The usual sftp wrapped by lftp utility is considerably faster.
export HOST=
export USER=
export PASS=
export RVA=/rds/project/jmmh2/rds-jmmh2-projects/olink_proteomics/scallop/SCALLOP-Seq/rva
lftp -c "open sftp://${USER}:${PASS}@${HOST}:/genetic_data/for_Grace; mirror -c -P=20 -R -v ${RVA}"
File download
We simply drop "-R" from above to have,
export HOST=
export USER=
export PASS=
export RVA=/rds/project/jmmh2/rds-jmmh2-projects/olink_proteomics/scallop/SCALLOP-Seq/rva
lftp -c "open sftp://${USER}:${PASS}@${HOST}:/genetic_data/for_Grace; mirror -c -P=20 -v ${RVA}"