Is ANNOVAR able to annotate VCF files imputed by BEAGLE?

[Jiny000]

Hi there,

I used ANNOVAR to annotate vcf file imputed by beagle:

~/software/annovar/table_annovar.pl  test.vcf  --vcfinput --outfile test.out --buildver TEST  ~/path/to/db  --protocol refGene --operation g -remove

However, all sites were put into test.out.invalid_input file.
To find out the reason, I did these test:
1.Use the un-imputed VCF file. The result was correct.
2.Change the “|” in GT such as "0|0" to "0/0".It also worked.

So whether it is "|" in imputed VCF file that caused the error? I am confused because I think ANNOVAR uses GT info as additional information which won't effect annotations.

[kaichop]

By default, table_annovar annotates variants, not genotypes, so it should be able to work on beagle output file as the genotype information is ignored. If you supply an example file with say 100 variants, I can take a look and see why it does not recognize "|"

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On Sat, Dec 14, 2024 at 4:16 AM Jingyao Li ***@***.***> wrote: Hi there, I used ANNOVAR to annotate vcf file imputed by beagle: ~/software/annovar/table_annovar.pl test.vcf --vcfinput --outfile test.out --buildver TEST ~/path/to/db --protocol refGene --operation g -remove However, all sites were put into test.out.invalid_input file. To find out the reason, I did these test: 1.Use the un-imputed VCF file. The result was correct. 2.Change the “|” in GT such as "0|0" to "0/0".It also worked. So whether it is "|" in imputed VCF file that caused the error? I am confused because I think ANNOVAR uses GT info as additional information which won't effect annotations. — Reply to this email directly, view it on GitHub <#268>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OENECLWAXIARVEE5HT2FPZP5AVCNFSM6AAAAABTTLOCL2VHI2DSMVQWIX3LMV43ASLTON2WKOZSG4ZTSNZSGE2TANY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>