Gavin Ha

Hi @udp3f The quality of the data seems really good and might not be the problem. Do you see this type of result for the rest of the chromosomes? If...

Hi @udp3f Based on the event in chr17, the normal estimate should not be 0.91. It should be less than 0.1. What are the estimates for the run with initializations...

Something funny is going on. It must be a bug. Would it be possible for you to share the `RData` file for the `ploidy=2, cluster01` solution? If so, please send...

Hi @guanghaoli By default, the script excludes chrY. If you are using the snakemake workflow, you can modify this in the `config.yaml` file. Otherwise, you may have to adjust your...

Hi @fpbarthel Yes, I was working with the team at the Broad to include files that would be compatible with the input format for TITAN. You should be able to...

Hi @fpbarthel Sorry I hadn't realized that original link was to Broad-specific workflows. Here are the instructions for using GATK4-ACNV that should be more useful: https://gatkforums.broadinstitute.org/gatk/discussion/7387/description-and-examples-of-the-steps-in-the-acnv-case-workflow You will want to...

Hi @fpbarthel and @chapmanb Thank you both for looking into this. > I feel confident using TITAN with the denoised segments from GATK4 as input, and the hets from `ModelSegments`....

> Hi Gavin > > I've been running the Titan snakemake workflow and would be grateful if you could clarify a few things for me: > > 1. In the...

Hi @d-henness My guess is that you have some noisy outliers that are being called as individual segments. You can either exclude these segments prior to PhyloWGS. You can also...

Hi @fpbarthel Thanks for reporting back on your experiences with TITAN. The `selectSolution` script is my custom script to determine the optimal ploidy and cluster combination. However, I have only...