strand error assignment

[asilvestris84]

Hi,
I don't undestrand why (hg39) chr4 39550356 39550356 T C
is annotated by annovar as chr4 39550356 39550356 T C ncRNA_intronic UGDH-AS1
if UGDH-AS1 is annotated on the strand + while SMIM14 is on the - strand.
please can you help me understand? Apparently there is an error in the strand to which the SNP has been assigned.
My command: /lustrehome/asilvestris/exe/annovar/table_annovar.pl --buildver hg38 --outfile annovar_ncbiRefSeqCurated --protocol ncbiRefSeqCurated,rmsk --operation g,r, index_ann /lustrehome/asilvestris/exe/annovar/humandb
Thanks
Alessandro

[jammywwh]

Hi, @asilvestris84
Try to add --argument "-separate", in your command.
/lustrehome/asilvestris/exe/annovar/table_annovar.pl --buildver hg38 --outfile annovar_ncbiRefSeqCurated --protocol ncbiRefSeqCurated,rmsk --operation g,r --argument "-separate", index_ann /lustrehome/asilvestris/exe/annovar/humandb
As described in https://annovar.openbioinformatics.org/en/latest/user-guide/gene/,

"The value of the first column takes the following precedence (as of December 2010 and later version of ANNOVAR): exonic = splicing > ncRNA> > UTR5/UTR3 > intron > upstream/downstream > intergenic."

SMIM14 gene: UTR3
UGDH-AS1 gene: ncRNA_intronic
So chr4 39550356 39550356 T C is annotated by annovar as ncRNA_intronic UGDH-AS1,
add --argument "-separate",, the variant will annotated as ncRNA_intronic;UTR3 UGDH-AS1;SMIM14.

I hope this answer helps you.
Jammy