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@@ -20,8 +20,8 @@ The command line program has several arguments which will be explained and highl
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### Output flags
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These flags will enable you to specify the desired output: HLA allele sequences, eplets or frequencies. The output can further be restricted by specifying alleles for which only the sequences, eplets and/or frequencies should be reported (see `-a` or `-A` under [Other arguments](#other-arguments)). Not all HLA loci are available for every type of output:
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*`-H, --HLA` Flag to indicate that HLA alleles should be saved as multiple sequence alignments in fasta format per locus. These allele frequencies are retrieved from [the IMGT/HLA database github](https://github.com/ANHIG/IMGTHLA).<br>*Supported loci: A, B, C, DRA, DRB1, DRB3, DRB4, DRB5, DRB345, DQA1, DQA2, DQB1, DPA1, DPB1*
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*`-E, --eplet` Flag to indicate that eplets should retrieved from [the eplet registry database](https://www.epregistry.com.br) and outputted them into three csv files containing a summary (`summary_table-eplets.csv`), allele-eplet associations (`allele_table-eplets.csv`) and residues per eplet (`residue_table-eplets.csv`).<br>*Supported loci: A, B, C, DRB1, DRB3, DRB4, DRB5, DRB345, DQA1, DQB1, DPA1, DPB1*
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*`-H, --HLA` Flag to indicate that HLA alleles should be saved as multiple sequence alignments in fasta format per locus. These allele frequencies are retrieved from [the IMGT/HLA database github](https://github.com/ANHIG/IMGTHLA).<br>*Supported loci: A, B, C, DRA, DRB1, DRB3, DRB4, DRB5, DRB345, DQA1, DQA2, DQB1, DPA1, DPB1, MICA, MICB*
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*`-E, --eplet` Flag to indicate that eplets should retrieved from [the eplet registry database](https://www.epregistry.com.br) and outputted them into three csv files containing a summary (`summary_table-eplets.csv`), allele-eplet associations (`allele_table-eplets.csv`) and residues per eplet (`residue_table-eplets.csv`).<br>*Supported loci: A, B, C, DRB1, DRB3, DRB4, DRB5, DRB345, DQA1, DQB1, DPA1, DPB1, MICA*
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*`-F, --frequency` Flag to indicate that HLA allele frequencies should be retrieved from [the allele frequency database](http://www.allelefrequencies.net) and outputted into two table files: One with the average allele frequency per region and the other globally (averaged over all (specified) regions). The total sample size is also calculated per row.<br>*Supported loci: A, B, C, DRB1, DQA1, DQB1, DPA1, DPB1*
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