Eric Talevich

See the method in InferCNV: https://github.com/broadinstitute/inferCNV/wiki/Bayesian-Network-Latent-Mixture-Model This method uses an existing R package, [rjags](https://cran.r-project.org/web/packages/rjags/index.html), to perform MCMC simulations. Functions are [here](https://github.com/broadinstitute/infercnv/blob/master/R/inferCNV_BayesNet.R) and the driver script is [here](https://github.com/broadinstitute/infercnv/blob/master/scripts/run_BayesNet.R). Either wrap this...

Makefile portability: use variables for Rscript and Python, and set --rscript-path explicitly

2

Via #661, change the test Makefile to be more portable: Similar to the current line 5 of the Makefile where the cnvkit command is specified, * define a variable `python=python`...

Error in WGS mode on yeast genome

2

From Biostars: https://www.biostars.org/p/364267/ (User) was trying to call CNV in yeast genomes by running cnvkit.py batch Sample1.bam Sample2.bam -n Control1.bam Control2.bam -m wgs -f sacCer.fasta --annotate refFlat.txt command, but ran...

Per: https://bioconda.github.io/contributor/linting.html#missing-run-exports

batch hybrid: Use autobin for target and antitarget bin sizes

1

Currently the autobin step is skipped for `-m hybrid` and the hard-coded default values are used instead. Trust autobin. May need to restructure the code so autobin is run regardless...