From 986f8e1659af180856c495fbf27ac8cd073d560c Mon Sep 17 00:00:00 2001 From: Andrew Roth Date: Wed, 10 Jun 2020 13:00:32 -0700 Subject: [PATCH] Update README.md --- README.md | 29 ++--------------------------- 1 file changed, 2 insertions(+), 27 deletions(-) diff --git a/README.md b/README.md index 8f09198..d5c4d37 100644 --- a/README.md +++ b/README.md @@ -72,36 +72,11 @@ Default value is 0.001 if column is not present. ### Running PyClone-VI -PyClone-VI analyses are broken into two parts. -First the model is fit using the `fit` command. -Second the fitted model is post-processed and a results file produced using the `write-results-file` command. - -Sampling can be run as follows -``` -phyclone run -i INPUT.tsv -t TRACE.pkl -``` -which will take the file `INPUT.tsv` as described above and write the trace file `TRACE.pkl` in a Python pickle format. - -The `-n` command can be used to control the number of iterations of sampling to perform. - -The `-b` command can be used to control the number of burnin iterations to perform. -> Note: burnin is done using a heuristic strategy of unconditional SMC. -All samples from the burnin are discarded as they will not target the posterior. - -The `-d` command can be used to select the emission density. -As in PyClone the `binomial` and `beta-binomial` densities are available. -> Note: Unlike PyClone, PhyClone does not estimate the precision parameter of the Beta-Binomial. -This parameter can be set with the --precision flag. - -To build the final results of PhyClone you can run the `consensus` command as follows. -``` -phyclone consensus -d INPUT.tsv -t TRACE.pkl -n TREE.nwk -o TABLE.tsv -``` -where `INPUT.tsv` and `TRACE.pkl` are the same as the previous step and `TREE.nwk` is the clone tree in newick format and `TABLE.tsv` the assignment of mutations to clones. +TODO # License -PhyClone is licensed under the GPL v3, see the LICENSE.txt file for details. +PyClone-VI is licensed under the GPL v3, see the LICENSE.txt file for details. # Versions