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Output

call-reads, call-consensus and call-contigs all generate three reports containing HLA star-allele type calls. Additionally, call-contigs produces fasta files of extracted sequences from the assembly. If out_prefix is given as a directory + prefix/samplename, output files will be joined to the prefix with underscore _.

File Description
{out_prefix}[_/]hifihla_summary.tsv Detailed file listing best call for each locus
{out_prefix}[_/]hifihla_report.tsv Simple tsv file listing calls for each locus
{out_prefix}[_/]hifihla_report.json Detailed results file, see below for example
{out_prefix}[_/]asm.contigs.h[12].fasta Extracted (full) assembly contigs aligning to MHC
{out_prefix}[_/]asm.contigs.h[12].fasta.fai FASTA index for contigs
{out_prefix}[_/]extracted.targets.h[12].fasta Extracted targets used for star-typing

Detailed summary tsv

This file reports the single best call and statistics for each query sequence in the sample.

Column Name Description
queryId Query sequence name
qLen Length of query sequence
nMatches Number of equivalent matches with same edit distance
gType Closest matching genomic accession
gPctId Percent matching bases of closest genomic match
gPctCov Percent coverage of closest genomic match
gEdit Edit distance to closest genomic match
cdnaType Closest matching coding sequence
exCovered Exons included in alignment
exEdit Edit distance to cDNA match
coverage HiFi read count of allele (call-reads only)
errRate Total error rate of HiFi reads (call-reads only)
Type Final type call

Final type call is determined by edit distance and exact matches to the query (nMatches). The final call is four field if the query sequences matches exactly and is the only exact match returned.

call-reads summary for HG002 (Class I):

queryId  qLen  nMatches  gType              gPctId  gPctCov  gEdit  cdnaType        exCovered        exEdit  coverage  errRate  Type
HLA-A_1  3503  1         HLA-A*01:01:01:01  100.0   100.0    0      HLA-A*01:01:01  1,2,3,4,5,6,7,8  0       15        0.00276  HLA-A*01:01:01:01
HLA-A_0  3517  1         HLA-A*26:01:01:01  100.0   100.0    0      HLA-A*26:01:01  1,2,3,4,5,6,7,8  0       13        0.00249  HLA-A*26:01:01:01
HLA-B_0  3855  1         HLA-B*35:08:01:01  100.0   100.0    0      HLA-B*35:08:01  1,2,3,4,5,6,7    0       18        0.00231  HLA-B*35:08:01:01
HLA-B_1  4070  1         HLA-B*38:01:01:01  100.0   100.0    0      HLA-B*38:01:01  1,2,3,4,5,6,7    0       10        0.00204  HLA-B*38:01:01:01
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       12        0.00135  HLA-C*04:01:01:06
HLA-C_1  4303  1         HLA-C*12:03:01:01  100.0   100.0    0      HLA-C*12:03:01  1,2,3,4,5,6,7,8  0       8         0.00215  HLA-C*12:03:01:01

call-contigs summary for HG00733:

queryId                                  qLen   nMatches  gType                 gPctId  gPctCov  gEdit  cdnaType           exCovered        exEdit  coverage  errRate  Type
HG00733#1#h1tg000070l_29911131_29915604  4474   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       1         N/A      HLA-A*24:02:01:01
HG00733#2#h2tg000008l_1854867_1859341    4475   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       1         N/A      HLA-A*30:02:01:01
HG00733#1#h1tg000070l_31324234_31329311  5078   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       1         N/A      HLA-B*35:02:01:02
HG00733#2#h2tg000008l_440231_445304      5074   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       1         N/A      HLA-B*18:01:01:01
HG00733#1#h1tg000070l_31239869_31245142  5274   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       1         N/A      HLA-C*04:01:01:06
HG00733#2#h2tg000008l_525397_530669      5273   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       1         N/A      HLA-C*05:01:01:01
HG00733#1#h1tg000070l_33003286_33014048  10763  1         HLA-DPA1*01:03:01:02  100.0   100.0    0      HLA-DPA1*01:03:01  1,2,3,4          0       1         N/A      HLA-DPA1*01:03:01:02
HG00733#2#h2tg000060l_26807522_26818289  10768  1         HLA-DPA1*02:01:01:01  100.0   100.0    0      HLA-DPA1*02:01:01  1,2,3,4          0       1         N/A      HLA-DPA1*02:01:01:01
HG00733#1#h1tg000070l_33014638_33027155  12518  1         HLA-DPB1*04:01:01:01  100.0   100.0    0      HLA-DPB1*04:01:01  1,2,3,4,5        0       1         N/A      HLA-DPB1*04:01:01:01
HG00733#2#h2tg000060l_26794480_26806932  12453  1         HLA-DPB1*11:01:01:01  100.0   100.0    0      HLA-DPB1*11:01:01  1,2,3,4,5        0       1         N/A      HLA-DPB1*11:01:01:01
HG00733#1#h1tg000070l_32583472_32591044  7573   1         HLA-DQA1*05:05:01:01  100.0   100.0    0      HLA-DQA1*05:05:01  1,2,3,4          0       1         N/A      HLA-DQA1*05:05:01:01
HG00733#2#h2tg000060l_27233443_27240904  7462   1         HLA-DQA1*05:01:01:01  100.0   100.0    0      HLA-DQA1*05:01:01  1,2,3,4          0       1         N/A      HLA-DQA1*05:01:01:01
HG00733#1#h1tg000070l_32600790_32608991  8202   1         HLA-DQB1*03:01:01:02  100.0   100.0    0      HLA-DQB1*03:01:01  1,2,3,4,5,6      0       1         N/A      HLA-DQB1*03:01:01:02
HG00733#2#h2tg000060l_27214264_27222723  8460   1         HLA-DQB1*02:01:01:01  100.0   100.0    0      HLA-DQB1*02:01:01  1,2,3,4,5,6      0       1         N/A      HLA-DQB1*02:01:01:01
HG00733#1#h1tg000070l_32526722_32541633  14912  1         HLA-DRB1*11:04:01:01  100.0   100.0    0      HLA-DRB1*11:04:01  1,2,3,4,5,6      0       1         N/A      HLA-DRB1*11:04:01:01
HG00733#2#h2tg000060l_27282742_27297652  14911  1         HLA-DRB1*03:01:01:02  100.0   100.0    0      HLA-DRB1*03:01:01  1,2,3,4,5,6      0       1         N/A      HLA-DRB1*03:01:01:02
HG00733#1#h1tg000070l_32462971_32477576  14606  1         HLA-DRB3*02:02:01:04  99.99   100.0    1      HLA-DRB3*02:02:01  1,2,3,4,5,6      0       1         N/A      HLA-DRB3*02:02:01
HG00733#2#h2tg000060l_27346699_27361303  14605  1         HLA-DRB3*02:02:01:01  100.0   100.0    0      HLA-DRB3*02:02:01  1,2,3,4,5,6      0       1         N/A      HLA-DRB3*02:02:01:01

Simple tsv format

This file is formatted for a quick view of top-level results. It is appropriate as input for downstream interpretation tools like pharmCAT.

$ column -t hifihla_report.tsv
HLA-A     *01:01:01:01/*26:01:01:01
HLA-B     *38:01:01:01/*35:08:01:01
HLA-C     *12:03:01:01/*04:01:01:06  

Detailed results json

Detailed results contain information on calls for each sequence typed. The json is structured in the following way:

 { sample_id: <sample_id>,
   hla_calls: {
        <locus>: {
                    <Record_id>: [
                       {
                        allele_id:      <imgt_accession>,
                        star_name:      <full_star_name>,
                        length:         <accession_seq_length>,
                        match_name:     <match_up_to_fields>,
                        query_start:    <query_aln_start>,
                        query_end:      <query_aln_end>,
                        covered_feat:   <aligned_features>,
                        not_covered:    <features_no_coverage>,
                        coding_diffs:   <total_exon_differences>,
                        noncode_eddist: <edit_dist_introns_utr>,
                        error_rate:     <total HiFi error rate (call-reads only)>,
                        coverage:       <Number of reads covering allele (call-reads only)>,
                        reads:          <HiFi read names used in analysis of allele (call-reads only)>,
                        differences: [
                             {
                                kind: <mismatch/insertion/deletion>,
                                pos:  <position>,
                                size: <variant_length>,
                                feat: <feature_containing_variant>                            
                             },
                             ...                        
                            ]                     
                        }                     
                    ],
                    ...
                }
                ...
            }
 }   

Extracting detailed results for a given locus can be done with the jq tool:

jq '.hla_calls | with_entries(select(.key == "HLA-DRB3"))' tmp2/hifihla_report.json

{
    "HLA-DRB3": [
          {
            "HG00733#1#h1tg000070l_32462971_32477576": [
              {
                "allele_id": "HLA22697",
                "star_name": "HLA-DRB3*02:02:01:04",
                "length": 12905,
                "match_name": "*02:02:01",
                "query_start": 0,
                "query_end": 12905,
                "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",
                  "UTR_3"
                ],
                "not_covered": [],
                "coding_diffs": 0,
                "noncode_eddist": 1,
                "error_rate": null,
                "coverage": 1,
                "reads": null,
                "differences": [
                  {
                    "kind": "Mismatch",
                    "pos": 8158,
                    "size": 1,
                    "feat": "Intron_2"
                  }
                ]
              }
            ],
            "HG00733#2#h2tg000060l_27346699_27361303": [
              {
                "allele_id": "HLA00895",
                "star_name": "HLA-DRB3*02:02:01:01",
                "length": 13588,
                "match_name": "*02:02:01:01",
                "query_start": 0,
                "query_end": 13588,
                "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",
                  "UTR_3"
                ],
                "not_covered": [],
                "coding_diffs": 0,
                "noncode_eddist": 0,
                "error_rate": null,
                "coverage": 1,
                "reads": null,
                "differences": []
            }
         ]
      }
   ]
}