Is it possible to remove patches from assembly?

Science
1

I am using gnomad 3.1.2 to extract SNPs. It is very important that these SNPs align with another customized database containing miRNA sequences.

Gnomad documentation on their assembly is weak. From this update, it appears they are using GRCH38.p13. Although, I can’t figure out if they are using the GenBank assembly (GCA_000001405.28) or the refseq assembly (GCF_000001305.39). If anyone knows, please comment.

The reason why this is important is simple… the patches are creating regions where the sequences don’t match between gnomad and the custom miRNA database.

Thus, I was wondering if hail has any built-in method to remove the patches and revert the assembly to its original form (e.g. GCA_000001405.15).

Thank you!

2

I believe it actually is a GenBank assembly. The fasta we used is at gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta and the first line of that suggests the chr1 accession number is AC:CM000663.2 which points me to GenBank - I don’t see the exact assembly accession number there, but it may be there somewhere