Hello everyone,
I'm attempting to annotate a VCF file using SNPEff. The annotation seems to be working fine, but I'm concerned about the number of warnings that I'm getting.
Exerpt from the verbose output:
WARNINGS: Some warning were detected
Warning type Number of warnings
INFO_REALIGN_3_PRIME 133110
WARNING_TRANSCRIPT_INCOMPLETE 115950
I checked into these warnings in the SNPEff documentation, and it seems like they may indicate problems with the reference, but I'm using SNPEff's own GRCm38 reference.
I thought part of the problem might stem from the fact that my VCFs are mm10, not GRCm38 (same build I know, but with different chromosome ids), so I tried changing the chromosome ids (e.g. chr1 to 1) but I got the same warnings.
I'm sure I must be overlooking something obvious but I can't determine what.
Can I just ignore these warnings and proceed with the resulting annotation? Or should I filter out the variants that are flagged with warnings (~25% of the variants)?
Thanks.
I'm attempting to annotate a VCF file using SNPEff. The annotation seems to be working fine, but I'm concerned about the number of warnings that I'm getting.
Exerpt from the verbose output:
WARNINGS: Some warning were detected
Warning type Number of warnings
INFO_REALIGN_3_PRIME 133110
WARNING_TRANSCRIPT_INCOMPLETE 115950
I checked into these warnings in the SNPEff documentation, and it seems like they may indicate problems with the reference, but I'm using SNPEff's own GRCm38 reference.
I thought part of the problem might stem from the fact that my VCFs are mm10, not GRCm38 (same build I know, but with different chromosome ids), so I tried changing the chromosome ids (e.g. chr1 to 1) but I got the same warnings.
I'm sure I must be overlooking something obvious but I can't determine what.
Can I just ignore these warnings and proceed with the resulting annotation? Or should I filter out the variants that are flagged with warnings (~25% of the variants)?
Thanks.
