call-reads accepts aligned HiFi reads in BAM format and calls HLA alleles directly from reads, without assembly.
Call HLA loci from an aligned BAM of HiFi reads
Usage: hifihla call-reads [OPTIONS] --abam <ALIGNED_READS>
Options:
-j, --threads <THREADS> Analysis threads [default: 1]
-v, --verbose... Enable verbose output
--log-level <LOG_LEVEL> Alternative to repeated -v/--verbose: set log level via key. [default: Warn]
-h, --help Print help
-V, --version Print version
Input Options:
-a, --abam <ALIGNED_READS> Input assembly aligned to GRCh38 (no alts)
-l, --loci [<LOCI>...] Input comma-sep loci to extract [default: all]
-d, --max_depth <MAX_DEPTH> Maximum reads per locus [default: 50]
-p, --partial Include partially-spanning reads
-t, --haplotypes <HAPLOTYPES> Haplotypes in sample [default: 2] [possible values: 1, 2]
-s, --seed <SEED> Random number seed for downsampling to max_depth [default: 42]
Output Options:
-o, --out_prefix <OUT_PREFIX> Output prefix
--outdir <OUTDIR> Output directory [deprecated]
-f, --full_length Full length IMGT records only (exclude exon-only records)
-x, --max_matches <MATCHES> Maximum matches in output report [default: 10]
-m, --min_allele_freq <MAF> Minimum allele frequency [default: 0.1]
-b, --min_cdf <MINCDF> Minimum binomial CDF to call het/hom [default: 0.001]
Presets:
--preset <PRESET> Sequence type presets [possible values: te, wgs]
--abamHiFi reads aligned to GRCH38 no alts.--lociHLA loci to call. Currently limited to HLA-A,HLA-B,HLA-C.--max_depthMaximim reads to use per locus. Reads are randomly downsampled if coverage > d.--partialInclude HiFi reads that do not fully span locus, but still span exon 2 (minimum requirement).--haplotypesExpected number of haploytypes in sample.--seedRandom number seed for downsampling and clustering.
--out_prefixOutput prefix, accepts a directory or a directory + prefix.--outdirOutput directory [deprecated].--full_lengthRestrict allele matches to full length IMGT records (exclude exon-only accessions).--max_matchesMaximum number of equivalent matches to list per query sequence.--min_allele_freqMinimum fraction of reads for minor allele. Clusters with lower frequency will be ignored.--min_cdfMinimum binomial CDF for minor allele. Clusters with lower CDF will be ignored.
Presets are convenience options for whole genome sequencing with long (>10kb) HiFi Readswgs or shorter (~5kb) Target Enrichment HiFi Reads te.
The only preset option at this time sets the -p flag for wgs, and no -p for te. Target Enrichment datasets tend to have higher coverage, so we filter for fully spanning reads.
Type Class I (HLA-A/-B/-C) alleles from HPRC HG00733 aligned WGS HiFi reads using 8 threads:
hifihla call-reads \
--preset wgs \
-j 8 \
-a HG00733.GRCh38_no_alts.bam \
-o 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
HLA-A_1 3502 1 HLA-A*24:02:01:01 100.0 100.0 0 HLA-A*24:02:01 1,2,3,4,5,6,7,8 0 9 0.00346 HLA-A*24:02:01:01
HLA-A_0 3503 1 HLA-A*30:02:01:01 100.0 100.0 0 HLA-A*30:02:01 1,2,3,4,5,6,7,8 0 25 0.00293 HLA-A*30:02:01:01
HLA-B_1 4081 1 HLA-B*18:01:01:01 100.0 100.0 0 HLA-B*18:01:01 1,2,3,4,5,6,7 0 16 0.00281 HLA-B*18:01:01:01
HLA-B_0 4085 1 HLA-B*35:02:01:02 100.0 100.0 0 HLA-B*35:02:01 1,2,3,4,5,6,7 0 18 0.00250 HLA-B*35:02:01:02
HLA-C_0 4264 1 HLA-C*04:01:01:06 100.0 100.0 0 HLA-C*04:01:01 1,2,3,4,5,6,7,8 0 20 0.00280 HLA-C*04:01:01:06
HLA-C_1 4303 1 HLA-C*05:01:01:01 100.0 100.0 0 HLA-C*05:01:01 1,2,3,4,5,6,7,8 0 12 0.00335 HLA-C*05:01:01:01
Type Class I alleles from targeted Twist Alliance Panels sequenced with PacBio HiFi:
hifihla call-reads \
--preset te \
-j 8 \
-a HG01190.GRCh38_noalt.deepvariant.haplotagged..bam \
-o my_output_dir
column -t my_output_dir/hifihla_summary.tsv
queryId qLen nMatches gType gPctId gPctCov gEdit cdnaType exCovered exEdit coverage errRate Type
HLA-A_1 3517 1 HLA-A*02:01:01:01 100.0 100.0 0 HLA-A*02:01:01 1,2,3,4,5,6,7,8 0 19 0.00108 HLA-A*02:01:01:01
HLA-A_0 3502 1 HLA-A*24:02:01:01 100.0 100.0 0 HLA-A*24:02:01 1,2,3,4,5,6,7,8 0 28 0.00213 HLA-A*24:02:01:01
HLA-B_1 3327 1 HLA-B*15:20 100.0 100.0 0 HLA-B*15:20 1,2,3,4,5,6,7 0 18 0.00107 HLA-B*15:20
HLA-B_0 4081 1 HLA-B*18:01:01:83 100.0 100.0 0 HLA-B*18:01:01 1,2,3,4,5,6,7 0 10 0.00059 HLA-B*18:01:01:83
HLA-C_0 4304 1 HLA-C*01:02:01:01 100.0 100.0 0 HLA-C*01:02:01 1,2,3,4,5,6,7,8 0 24 0.00121 HLA-C*01:02:01:01
HLA-C_1 4318 1 HLA-C*07:01:01:16 100.0 100.0 0 HLA-C*07:01:01 1,2,3,4,5,6,7,8 0 26 0.00205 HLA-C*07:01:01:16
Force call only a single, full-length HLA-A haplotype using at most 15 reads:
hifihla call-reads \
-d 15 \
-t 1 \
-f \
-l HLA-A \
-a NA12889.GRCH38.haplotagged.bam \
-o out_dir/my_sample
cat out_dir/my_sample_hifihla_report.json
{
"sample_id": "NA12889.GRCh38.haplotagged",
"version": "hifihla 0.3.0;IPD-IMGT/HLA 3.55 (2024-01)",
"hla_calls": {
"HLA-A": [
{
"HLA-A_0": [
{
"allele_id": "HLA00037",
"star_name": "HLA-A*03:01:01:01",
"length": 3502,
"match_name": "*03:01:01:01",
"query_start": 0,
"query_end": 3502,
"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": 0.0023986294,
"coverage": 15,
"reads": [
"m54329U_230312_191124/80677293/ccs",
"m84046_230327_223715_s3/52499911/ccs",
"m54329U_230314_044350/92145583/ccs",
"m54329U_230311_094504/134349275/ccs",
"m84046_230327_223715_s3/41027584/ccs",
"m84046_230327_223715_s3/80090755/ccs",
"m84046_230327_223715_s3/132322013/ccs",
"m84046_230327_223715_s3/80871474/ccs",
"m84046_230327_223715_s3/41226855/ccs",
"m54329U_230312_191124/63046676/ccs",
"m54329U_230311_094504/31064736/ccs",
"m54329U_230312_191124/56625320/ccs",
"m84046_230327_223715_s3/38012954/ccs",
"m84046_230327_223715_s3/23856426/ccs",
"m54329U_230314_044350/129892658/ccs"
],
"differences": []
}
]
}
]
}
}