Follow this link to see a video of the User Interface:
https://drive.google.com/file/d/1cmn083ruUX5KCIYWPqQLlW3a0bgpAm07/view
Clone and enter this directory, and then:
bash install.sh
bash build-vue-app.sh
Only installation on Linux x86_64 is currently supported.
Assuming one has access to the protected environment on the CHPC at University of Utah:
bash tests/test.sh
Follow the instructions at the command line to view a web app that visualizes mutation counts as a function of genomic coordinate.
Assuming that the path to the constraint-tools
directory on your filesystem is ${root}
, usage is:
PATH="${root}:$PATH"
constraint-tools [SUB_COMMAND] REQUIRED_ARGUMENTS
Valid sub-commands are:
train
estimate kmer-dependent mutation probabilities
visualize
start a web app that visualizes mutation counts as a function of genomic coordinate
predict
call genomic regions predicted to be under negative selection [not yet implemented]
Required arguments for train
are:
--genome STR
Path to the reference fasta.
A "samtools faidx" index is expected to be present at the same path.
--region STR
Samtools-style specification of a genomic interval (see examples in tests directory).
--mutations STR
Path to a set of mutations specified in Mutation Annotation Format.
A "tabix" index is expected to be present at the same path.
--kmer-size INT
Size of kmer to use in model.
--output STR
Path to a directory to store results in.
This produces a specification of the sequence-dependent mutation model in json format, viewable using, e.g.,
${root}/bin/jq . ${output}/<json file>
Required arguments for visualize
are:
--model STR
Path to the model produced by the train sub-command (in json format)
--port INT
The port to serve the web-app on
Assuming one has access to the protected environment on the CHPC at University of Utah, then sorted, block-compressed, and indexed vcf, maf, gtf and fasta files can be found at:
/scratch/ucgd/lustre-work/quinlan/u6018199/constraint-tools/data
Changes to the vue-app
directory necessitate rebuilding the vue app by running
bash build-vue-app.sh
- specification: https://docs.gdc.cancer.gov/Data/File_Formats/MAF_Format/
- minimal example: https://github.com/mskcc/vcf2maf/blob/main/data/minimalist_test_maf.tsv
- tooling:
- gotchas: https://www.biostars.org/p/69222/