Don't understand the meaning of "no-comp-alleles"

[lwtan90]

Hi,

I have read all your responses to question relating to "VCF" liftovers. I understand the literal meaning of "CrossMap does NOT check if the reference allele is different from the alternate allele".

My questions are:

• Is the alternate allele here referring to the ALT column in VCF?
• the reference / alternate check happens before/after liftover?
• If it is post-liftover, is it saying that crossmap doesnt do liftover for the alternate allele entry in the VCF?
• If they are the same/different, how should we intepret it?

Thank you for this tool!

Wilson