An error is thrown during custom annotation file creation that does not align with the UCSC Genome Browser

[RoriCremer]

Version: 3.14 from docker image. Reference: hg38 Updated datasources using the Download tool in NIRVANA? Yes, from the same docker image (tag 3.14).

An error is thrown during custom annotation file creation that does not align with the expected reference

When creating a custom annotation (dotnet customvar), the following error is thrown:

ERROR: The provided reference allele GTGN at chr3:16902880 is different from GTGG in the reference genome sequence.

The documentation around Reference Base Checking during the creation of the custom annotation Nirvana file format seems to match with this error being thrown

However, this Nirvana error message seems to be incorrect.  There is an "N" at chr3:16902883 according to UCSC Genome Browser. (GRCh38.p13)

The input TSV file (for custom annotations) looked like this at that position:

contig position ref alt(s) chr3 16902879 TGTGN CGTGN,GGTGN,T chr3 16902881 TGN CGN,TGTGTGTGTGTGCGN,TGTGTGTGTGCGN,TGCGN,TGTGTGTGTGTGTGCGN,TGTGCGCGN,TGTGTGTGTGTGTGTGCGN,TGTGTGCGN,TGTGTGTGTGTGTGTGTGTGTGCGN,TGTGTGTGCGN,TGTGCGN,TGTGTGTGTGTGTGTGTGTGCGN,TGTGTGTGTGCGCGN,TGTGTGTGTGTGTGTGTGTGTGTGCGN,TGTGTGTGTGTGTGTGTGTGTGTGTGCGN,TGTGTGTGTGTGTGTGTGCGN,TGTGTGTGTGTGTGCGCGN,TGCGCGN,TGTGTGCGCGN,TGTGTGTGCGCGN,TGTGTGTGTGTGCGCGN,TGTGTGTGTGTGTGTGTGTGTGTGTGTGCGN,TGCGCGCGN,T,TGTGTGCGCGCGCGN,TGTGTGTGTGTGTGTGTGCGCGN,TGTGTGCGCGCGN

Is there a way to disable Reference Base Checking?

[heseber]

I think there is:

❯ bin/Release/netcoreapp3.1/SAUtils CustomVar -h
---------------------------------------------------------------------------
SAUtils                                             (c) 2021 Illumina, Inc.
Stromberg, Roy, Lajugie, Jiang, Li, and Kang                         3.17.0
---------------------------------------------------------------------------

USAGE: dotnet SAUtils.dll customvar [options]
Creates a supplementary variant annotation database from a custom input file

OPTIONS:
      --ref, -r <VALUE>      compressed reference sequence file
      --in, -i <VALUE>       custom TSV file path
      --out, -o <VALUE>      output directory
      --skip-ref             skip ref base validation
      --help, -h             displays the help menu
      --version, -v          displays the version

[rajatshuvro]

Thanks @heseber .