Is hg38 on the multiz 30-way alignment inaccurate?

Is hg38 on the multiz 30-way alignment inaccurate?

0

Hello,

I have a general question: Is it possible that the multiz 30-way alignment is inaccurate? I am looking for specific hg38 sequences in the blocks (I am using BLAT retrieved coordinates, with PHAST to parse the maf blocks), and the sequences I am getting do not match the sequences I see from ensembl/ their coordinates. Trying to figure out why this may be, and how to deal with this issue.

My files say ##maf version=1 scoring=roast.v3.3


maf


UCSC


PHAST


multiz

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