Tigger alleles not found

[Gisela Gabernet Garriga]

Hi, I’m having an issue with Tigger version 1.0.0 and the genotypeFasta function. I am running:

  library(tigger)
  library(alakazam)

  db <- read.table("input.tsv", header=TRUE, sep="\t")

  db_fasta <- readIgFasta("IMGT_ighv.fasta", strip_down_name = TRUE)

  gt <- inferGenotype(db, v_call = "v_call", seq="sequence_alignment",find_unmutated = FALSE)

  gtseq <- genotypeFasta(gt, db_fasta)

And getting the error:

Error in genotypeFasta(gt, db_fasta) :
  The following genotype alleles were not found in germline_db: IGHV3-23D*01, IGHV3-64D*09

However, the alleles are present in the provided imgtdb_base/human/vdj/imgt_human_IGHV.fasta:

>AC244492|IGHV3-23D*01|Homo_sapiens|F|V-REGION|21795..22090|296 nt|1| | | | |296+24=320| | |
>MN337625|IGHV3-64D*09|Homo_sapiens|F|V-REGION|348..643|296 nt|1| | | | |296+24=320| | |

The employed input.tsv and imgt fasta files are attached.

[ssnn]

Hi @Gisela Gabernet Garriga I fixed the issue in commit 9b023e2. Please, install the most recent version of tigger from the repo, and let me know if you still have issues.

[Gisela Gabernet Garriga]

Hi Susanna @ssnn ,
great, thanks a lot. I will test it asap and report back

[ssnn]

@Gisela Gabernet Garriga I am going to close this as resolved. Please, reopen if needed.