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usage.md

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Usage

hifihla has four subcommands:

Usage: hifihla <COMMAND>

Commands:
  call-reads      Call HLA loci from an aligned BAM of HiFi reads
  call-contigs    Extract HLA loci from assembled MHC contigs & call star alleles on extracted sequences
  call-consensus  Call HLA Star (*) alleles from consensus sequences
  align-imgt      Align queries to IMGT/HLA genomic accession sequences
  help            Print this message or the help of the given subcommand(s)

Options:
  -h, --help     Print help
  -V, --version  Print version

Subcommand Inputs

Subcommand Input Type File types Description
call-reads Aligned HiFi reads BAM Call Class I (ABC) from HiFi reads aligned to GRCH38 no alts
call-contigs Aligned assembly; unaligned contigs BAM, FASTA(.gz) Extract and Call HLA loci from assembled MHC contigs
call-consensus Amplicon/Isoseq consensus FASTA Call HLA alleles from consensus sequences (e.g. amplicon assays)
align-imgt Sequence/IMGT accessions FASTA Compare sequences in fasta format or database sequences to specific IMGT/HLA genomic alleles