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Genome Nexus sometimes annotates SNV as ONP #33

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thomasyu888 opened this issue Jan 16, 2021 · 4 comments
Open

Genome Nexus sometimes annotates SNV as ONP #33

thomasyu888 opened this issue Jan 16, 2021 · 4 comments

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@thomasyu888
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thomasyu888 commented Jan 16, 2021

  • 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

@inodb inodb self-assigned this Jan 22, 2021
@n1zea144 n1zea144 assigned ao508 and thomasyu888 and unassigned inodb and ao508 Jan 22, 2021
@thomasyu888
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Taking a quick look at this, i reach similar initial conclusions as #32

@thomasyu888 thomasyu888 removed their assignment Jan 23, 2021
@as1000
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as1000 commented Feb 10, 2021

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

@ao508
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ao508 commented Mar 17, 2021

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

@sheridancbio
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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.

@inodb inodb assigned sheridancbio and unassigned inodb Mar 29, 2021
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