Genome Nexus sometimes annotates SNV as ONP

[thomasyu888]

• Input:
  input.txt

• Intermediate files: annotation-tools intermediate files I must add the .txt at the end or github won't allow me to upload these. My understanding it the input.txt.temp.annotated.txt is the output from Genome Nexus. But because the annotation-tools allows us to include a directory with a list of mafs or vcfs, it annotates each one of those files separately. processed.txt is all of these merged.
  input.txt.temp.annotated.txt
  input.txt.temp.txt

• processed:
  processed.txt

[thomasyu888]

Taking a quick look at this, i reach similar initial conclusions as #32

[as1000]

Seems to be the same problem as #32, regarding the reference allele.

[ao508]

Is the variant in the intermediate file labeled as ONP or is the annotated record coming back from Genome Nexus as ONP

[sheridancbio]

Similar to my recent comment in #32, These two cases include Reference_Allele inputs which are discrepant from the UCSC Browser results when querying these positions (believed to represent the latest/final version of the hg19/GRCh37 genome assembly, and to be consistent with the VEP cache version in use in genome nexus):

Chromosome	Start_Position	Reference_Allele	UCSC_browser_hg19	Tumor_Seq_Allele2	Tumor_Sample_Barcode
17	7578456	TGGCGCG	GCGGACG	TGGCAAG	SAGE-1
17	7578397	GAA	TGG	TCC	SAGE-1

Because the reported Reference_Allele does not match the allele in the reference genome assembly in use by VEP, we are confirming that these cases should have been marked with a failure to annotate, maybe giving additional information that the cause was a mismatch in the Reference_allele column.