Mutations in common not found across yamls

[schianta]

I'm getting an error saying that there are no mutation id's in common, but when I look in the yaml file I can find mutations in common (example picture attached). Do you have any suggestions for why this might be happening or how to fix the issue?

[schianta]

pyclone_config_template_to_base_on.txt Attached is the config file, am I passing parameters incorrectly?

[aroth85]

Is the mutation in the YAML file for every single sample?

On Tue, 4 Jun 2019 at 16:45, schianta notifications@github.com wrote:

pyclone_config_template_to_base_on.txt https://github.com/aroth85/pyclone/files/3252965/pyclone_config_template_to_base_on.txt Attached is the config file, am I passing parameters incorrectly?

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[schianta]

Thank you so much for your quick response! I limited my analysis to samples from just the primary tumor, and pyclone ran to completion. However, it appears to have only conducted its analysis on 18 variants that were clonal across all the samples, and did not look at subclonal variants (see image below). All the yamls have over 100 mutation IDs specified, yet this analysis is only looking at 18. Is there some default that I need to override for subclonal variants to be considered?