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Illumina / Nirvana

The nimble & robust variant annotator
https://illumina.github.io/NirvanaDocumentation/
GNU General Public License v3.0
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SAUtils.dll custom database script failing #120

Open GH-MStamboulian opened 8 months ago

GH-MStamboulian commented 8 months ago

Hi, Im getting this error when trying to make my own database using the SAUtils.dll file... there error is below, I dont even have any entry at chromosome3 position 10183802, why do I get this error?

ERROR: Conflicting entries for items at chr3:10183802 for alleles T >

GH-MStamboulian commented 7 months ago

okay so I encountered another case which im unable to resolve,

Im using SAUtills file customvar functionality and constructing a database from the latest dbsnp download and the following two entries are giving me conflicts with the code:

#title=Sirius_v1.2_dbsnp
#assembly=GRCh37
#matchVariantsBy=allele
#CHROM  POS     REF     ALT     dbsnp_id        gene
#categories     .       .       .       .       .
#descriptions   .       .       .       .       .
#type   .       .       .       string  string
chr1    27107263        T       TC      rs551176418, rs369896037
chr1    27107272        C       CC      rs3841356

can you please help me understand what the logic for your script is here? I believe the block of code thats throwing off the error is here: https://github.com/Illumina/Nirvana/blob/main/SAUtils/DataStructures/SuppDataUtilities.cs#L69-L86C22

The code is somehow mapping these two loci to the same variant, eventhough I did left align and normalize the dbSNP VCF before feeding it as input.

@rajatshuvro @shulik7 @yujiang02