Snakemake workflow makes Titan assume male gender regardless of how config.yaml file is configured.

[d-henness]

As far as I can tell, changing the sex option in the config.yaml file does not actually change anything about the calculation. The --gender option does not appear in the shell command for runTitanCNA rule, so titanCNA.R will always use the default gender which is male. Was this intentional? Is there some reason we shouldn't be specifying the gender?

[gavinha]

Hi @d-henness

You're correct - in the snakemake pipeline the gender/sex options are not currently being used and defaults to male which excludes chrX.

I was in the middle of adding the feature to predict the gender from the ichorCNA analysis so that users can use None if the cohort includes both males and females.

For now, I will enable the user to use male or female but this will not work for cohorts with both.

[d-henness]

Thank you @gavinha. It would be helpful to allow the workflow to run both of these. Perhaps something could be added to the samples.yaml file such as

samples:
  tumor_sample_1:  /path/to/bam/tumor.bam
  normal_sample_1:  /path/to/bam/normal.bam

pairings:
  tumor_sample_1:  normal_sample_1

gender:
  tumor_sample_1: 'male' 

The gender field could be optional and default to male if not present so as not to interrupt workflows based on older versions. I can make up a pull request for this.