Since GRCh37, the reference has included alt loci, and those alt loci have come with GRC-created alignments back to the primary assembly. Those alignments are available in two formats, as described in ftp://ftp.ncbi.nih.gov/genbank/genomes/Eukaryotes/vertebrates_mammals/Homo_sapiens/GRCh38.p2/README_ASSEMBLIES:
8. alignments/{scaffold accession.version}_{chromosome accession.version}.asn
Files providing alignments of the alternate loci or patch scaffolds to the corresponding primary assembly chromosome, in ASN.1 format. These alignments indicate how the alternate loci and patch scaffold sequences differ from the chromosomes of the primary assembly. [Note: some older files do not have versions in the file names.]9. alignments/{{scaffold accession.version}_{chromosome accession.version}.gff Files providing alignments of the alternate loci or patch scaffolds to the corresponding primary assembly chromosome, in CIGAR format embedded within a GFF format file. These alignments indicate how the alternate loci and patch scaffold sequences differ from the chromosomes of the primary assembly. [Note: some older files do not have versions in the file names.]
However, the documentation for the assembly does not appear to explain how these alignments are created. Is the GRC running some sort of alignment tool? Are the alignments produced by hand? If I wanted to replicate the alignments, what would I do?
I ask because I recently submitted a paper in which I used the alignments, and one of the reviewers wanted to know how I had gotten those alignments and how they were put together.
