Feature request: option to ignore sex chromosomes? about goleft

[brentp]

that's great to hear. You should just be able to specify --sex "" . If that's not the case with the latest release, let me know and I'll have a look.

[roblanf]

Perfect. Works as you said. Thanks for clarifying. Perhaps worth a note in the docs somewhere (though maybe I missed it).

[brentp]

good idea. I added a note to the help indicating how to unset like that.

please let me know any other issues like this as I've mostly tested with human data.

[roblanf]

will do - so far so good though. Nice docs, binary runs out of the box, etc.

[roblanf]

I guess the best thing for non-human analyses here would be to just add something to the error message. I think most people will do what I did, which is copy and paste your example from the readme, and see what happens.

When I did that, I got the error that goleft couldn't find the X and Y chromosomes. If you added to that error the information on setting --sex "" to ignore sex chromosomes, that would be really helpful.

Even better - if you can't find X and Y chromosomes, just ignore sex chromosomes and print a warning?

[brentp]

I have made this a warning for now if --sex is the default and neither is found. The warning indicates how to set --sex to avoid the message.
This will be out in the next release, probably next week.
Thanks again.