Perfectly aligned to means that the aligned site in the target genome is the same nucleotide as the reference genome.
What is the target genome and reference genome ? what is MAF format ?
Here it is https://genome.ucsc.edu/FAQ/FAQformat.html#format5
Hi , I had a similar problem and have a very imperfect solution. PHAST (http://compgen.cshl.edu/phast/) provides a utility called maf_parse which can get an maf column for a bed file entry. I created a bed file for entire genome with each entry being 1 base pair. Then I used maf_parse to get maf columns for this bed. The entries where the nucleotides match should be the ones you want.
That is awesome. I happen to think of using maf_parse too. Thank you a lot.
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