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

[liguowang]

Is the alternate allele here referring to the ALT column in VCF? Yes

The reference / alternate check happens before/after liftover? After. The REF allele will be extracted from the reference genome user provided. ALT allele(s) will be kept as is.

If it is post-liftover, is it saying that crossmap doesnt do liftover for the alternate allele entry in the VCF? Please see my answer above. CrossMap does not change ALT allele(s). However, Crossmap will perform a reverse complement if the DNA strand is reversed during liftover.

If they are the same/different, how should we intepret it? If "--no-comp-alleles" is set, after liftover, REF=ALT, you need to remove it manually; If "--no-comp-alleles" is NOT set, CrossMap will filter out such variants. In my opinion, such a variant is technically not a variant anymore if REF=ALT; therefore, it should be removed.

I hope this helps you.