Correct use of --ploidy-chr flag

[leahkemp]

Hello! Thanks for providing this software!

Quick question, what is the correct way to use the --ploidy-chr flag for an XX and XY sample?

I imagined --ploidy-chr chrX:1,chrY:1 for XY and --ploidy-chr chrX:2,chrY:0 for XX but spectre errors out when I pass chrY:0.

Aplogies if I'm missing something obvious

[philippesanio]

Hi @leahkemp

Thank you for raising this question! For XX samples, you do not need to specify the ploidy state of chrY, because Spectre is using the blacklist that excludes chrY by default from any analysis. If you want to include chrY, you will need to remove the chrY region from the blacklist.

Assuming your sample is by default ploidy 2, you would not even need to specify the --ploidy-chr flag, as it would be set by default to ploidy 2. However, if you want to specifically set this flag, you would just need to set the flag to --ploidy-chr chrX:2

I hope this helps! Best, Philippe

[leahkemp]

Hi Phillipe,

Thanks for your help!

That makes sense, I didn't appreciate that the entirety of chrY was excluded from analysis/included in the blacklist.

Leah