call-consensus accepts a FASTA file of sequences and attempts to find the closest matching allele in the IMGT/HLA database. It is assumed that each FASTA record is a single locus.
Optionally call star alleles using exon sequence only.
Call HLA Star (*) alleles from consensus sequences
Usage: hifihla call-consensus [OPTIONS] --fasta <FASTA>
Options:
-f, --fasta <FASTA> Input fasta file of consensus sequences
-o, --out_prefix <OUT_PREFIX> Output prefix
--outdir <OUTDIR> Output directory [deprecated]
-c, --cdna Enable cDNA-only calling
-e, --exon2 Require Exon2 in query sequence
-l, --full_length Full length IMGT records only
-j, --threads <THREADS> Analysis threads [default: 1]
-x, --max_matches <MATCHES> Maximum equivalent matches per query in report [default: 10]
-v, --verbose... Enable verbose output
--log-level <LOG_LEVEL> Alternative to repeated -v/--verbose: set log level via key.
-h, --help Print help
-V, --version Print version
--fastaFasta file of consensus query sequences. Only one allele per query sequence.--out_prefixOutput prefix, accepts a directory or a directory + prefix.--outdirOutput directory [deprecated].--cdnaCall and report only coding regions (cdna). Can be used for either DNA or RNA sequences.--exon2Require exon 2 in query. This may reduce search space.--max_matchesOnly report up to this number of matches in the json report.
Type HLA consensus sequences, for example from HiFi amplicon consensus with pbaa:
hifihla call-consensus \
--fasta pbaa_12878-HG001_passed_cluster_sequences.fasta \
--out_prefix out_dir/my_sample
column -t out_dir/my_sample_hifihla_summary.tsv
queryId qLen nMatches gType gPctId gPctCov gEdit cdnaType exCovered exEdit coverage errRate Type
sample-12878-HG001_guide-HLA-A_cluster-0_ReadCount-1023 3098 5 HLA-A*01:01:01:01 100.0 88.43 0 HLA-A*01:01:01 1,2,3,4,5,6,7,8 0 1 N/A HLA-A*01:01:01
sample-12878-HG001_guide-HLA-A_cluster-1_ReadCount-999 3098 3 HLA-A*11:01:01:01 100.0 88.43 0 HLA-A*11:01:01 1,2,3,4,5,6,7,8 0 1 N/A HLA-A*11:01:01
sample-12878-HG001_guide-HLA-B_cluster-1_ReadCount-399 3354 7 HLA-B*08:01:01:01 100.0 81.69 0 HLA-B*08:01:01 1,2,3,4,5,6,7 0 1 N/A HLA-B*08:01:01
sample-12878-HG001_guide-HLA-B_cluster-0_ReadCount-481 3363 1 HLA-B*56:01:01:04 100.0 86.53 0 HLA-B*56:01:01 1,2,3,4,5,6,7 0 1 N/A HLA-B*56:01:01:04
sample-12878-HG001_guide-HLA-C_cluster-0_ReadCount-541 3384 6 HLA-C*01:02:01:01 100.0 78.62 0 HLA-C*01:02:01 1,2,3,4,5,6,7,8 0 1 N/A HLA-C*01:02:01
sample-12878-HG001_guide-HLA-C_cluster-1_ReadCount-484 3389 6 HLA-C*07:01:01:01 100.0 78.48 0 HLA-C*07:01:01 1,2,3,4,5,6,7,8 0 1 N/A HLA-C*07:01:01
sample-12878-HG001_guide-HLA-DPB1_cluster-1_ReadCount-348 5824 33 HLA-DPB1*04:01:01:01 100.0 50.52 0 HLA-DPB1*04:01:01 2,3,4,5 0 1 N/A HLA-DPB1*04:01:01
sample-12878-HG001_guide-HLA-DPB1_cluster-0_ReadCount-475 5760 7 HLA-DPB1*14:01:01:01 100.0 50.23 0 HLA-DPB1*14:01:01 2,3,4,5 0 1 N/A HLA-DPB1*14:01:01
sample-12878-HG001_guide-HLA-DQB1_cluster-1_ReadCount-2032 4076 12 HLA-DQB1*02:01:01:01 100.0 54.49 0 HLA-DQB1*02:01:01 2,3,4 0 1 N/A HLA-DQB1*02:01:01
sample-12878-HG001_guide-HLA-DQB1_cluster-0_ReadCount-3740 3703 14 HLA-DQB1*05:01:01:02 100.0 52.22 0 HLA-DQB1*05:01:01 2,3,4 0 1 N/A HLA-DQB1*05:01:01
sample-12878-HG001_guide-HLA-DRB1_cluster-1_ReadCount-1011 3900 15 HLA-DRB1*01:01:01:01 100.0 35.13 0 HLA-DRB1*01:01:01 2,3,4 0 1 N/A HLA-DRB1*01:01:01
sample-12878-HG001_guide-HLA-DRB1_cluster-0_ReadCount-2022 3646 14 HLA-DRB1*03:01:01:01 100.0 26.21 0 HLA-DRB1*03:01:01 2,3,4 0 1 N/A HLA-DRB1*03:01:01
Note that query sequences that match >1 allele are not labeled as four-field matches because the actual call is ambiguous. This can happen when differences between alleles are outside the amplified region. For example, HLA-A_cluster-1 above matches three alleles perfectly over the amplified range. All three matches are listed in the json.
jq '.. | objects | to_entries | .[] | select(.key == "sample-12878-HG001_guide-HLA-A_cluster-1_ReadCount-999")' my_sample_hifihla_report.json
{
"key": "sample-12878-HG001_guide-HLA-A_cluster-1_ReadCount-999",
"value": [
{
"allele_id": "HLA00043",
"star_name": "HLA-A*11:01:01:01",
"length": 3503,
"match_name": "*11:01:01",
"query_start": 182,
"query_end": 3280,
"covered_feat": [
"UTR_5",
"Exon_1",
"Intron_1",
"Exon_2",
"Intron_2",
"Exon_3",
"Intron_3",
"Exon_4",
"Intron_4",
"Exon_5",
"Intron_5",
"Exon_6",
"Intron_6",
"Exon_7",
"Intron_7",
"Exon_8",
"UTR_3"
],
"not_covered": [],
"coding_diffs": 0,
"noncode_eddist": 0,
"error_rate": null,
"coverage": 1,
"reads": null,
"differences": []
},
{
"allele_id": "HLA32930",
"star_name": "HLA-A*11:01:01:75",
"length": 3503,
"match_name": "*11:01:01",
"query_start": 182,
"query_end": 3280,
"covered_feat": [
"UTR_5",
"Exon_1",
"Intron_1",
"Exon_2",
"Intron_2",
"Exon_3",
"Intron_3",
"Exon_4",
"Intron_4",
"Exon_5",
"Intron_5",
"Exon_6",
"Intron_6",
"Exon_7",
"Intron_7",
"Exon_8",
"UTR_3"
],
"not_covered": [],
"coding_diffs": 0,
"noncode_eddist": 0,
"error_rate": null,
"coverage": 1,
"reads": null,
"differences": []
},
{
"allele_id": "HLA38435",
"star_name": "HLA-A*11:01:01:88",
"length": 3503,
"match_name": "*11:01:01",
"query_start": 182,
"query_end": 3280,
"covered_feat": [
"UTR_5",
"Exon_1",
"Intron_1",
"Exon_2",
"Intron_2",
"Exon_3",
"Intron_3",
"Exon_4",
"Intron_4",
"Exon_5",
"Intron_5",
"Exon_6",
"Intron_6",
"Exon_7",
"Intron_7",
"Exon_8",
"UTR_3"
],
"not_covered": [],
"coding_diffs": 0,
"noncode_eddist": 0,
"error_rate": null,
"coverage": 1,
"reads": null,
"differences": []
}
]
}