Qustions about step run CalicoST

[vincentguo0418]

Hello Dr.Ma,

I have three questions:

1. How to determine the value of n_clones in HMRF configurations?
2. I've been running the command “OMP_NUM_THREADS=100 python calicost_main.py -c configuration_cna” for 4 days, and it hasn't finished yet. My dataset consists of 8,298 pure tumor cells, 24K SNPs, and the possorted_genome_bam.bam file is 140GB. Approximately how long should this take? Are there any ways to speed it up?
3. If I have SNPs called from adjacent samples via WES (Whole Exome Sequencing), would you recommend filtering the SNPs called from SRT data with these WES-derived SNPs before running calicost_main.py?

Thanks a lot!

Best,
Vincent