Missing allele frequencies were annotated when using 1000g2015eas about doc-annovar

[fanwayne]

I just extracted the data from the zip file. I was not sure whether it is correct

[kaichop]

Did you check the output file? The output is written to the file ifit_hg38_bin_annovar.hg38_multianno.txt

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On Mon, Aug 26, 2024 at 10:54 PM fanwayne ***@***.***> wrote: table_annovar.pl ifit_hg38_bin.vcf $HOME/../../mnt/d/BaiduSyncdisk/biodata/humandb/ -buildver hg38 -out ifit_hg38_bin_annovar -remove -protocol refGene,ensGene,1000g2015aug_eas -operation g,g,f -nastring . -xref ~/annovar/example/gene_fullxref.txt -vcfinput My code was shown above. This running code did not prompt any errors or warning. But I just got nothing after running this code. Could you please help me with this issue? Many thanks! screenshot20240827105324.png (view on web) <https://github.com/user-attachments/assets/442f3e62-8863-4317-a104-1ef62df72b55> — Reply to this email directly, view it on GitHub <#251>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OCUMRFPQ2ZMYPS4CUTZTPS5RAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DQMJUG4ZDKNY> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[fanwayne]

Did you check the output file? The output is written to the file ifit_hg38_bin_annovar.hg38_multianno.txt
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On Mon, Aug 26, 2024 at 10:54 PM fanwayne @.> wrote: table_annovar.pl ifit_hg38_bin.vcf $HOME/../../mnt/d/BaiduSyncdisk/biodata/humandb/ -buildver hg38 -out ifit_hg38_bin_annovar -remove -protocol refGene,ensGene,1000g2015aug_eas -operation g,g,f -nastring . -xref ~/annovar/example/gene_fullxref.txt -vcfinput My code was shown above. This running code did not prompt any errors or warning. But I just got nothing after running this code. Could you please help me with this issue? Many thanks! screenshot20240827105324.png (view on web) https://github.com/user-attachments/assets/442f3e62-8863-4317-a104-1ef62df72b55 — Reply to this email directly, view it on GitHub <#251>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OCUMRFPQ2ZMYPS4CUTZTPS5RAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DQMJUG4ZDKNY . You are receiving this because you are subscribed to this thread.Message ID: @.>

Yes, the field was all missing.

[fanwayne]

Did you check the output file? The output is written to the file ifit_hg38_bin_annovar.hg38_multianno.txt
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On Mon, Aug 26, 2024 at 10:54 PM fanwayne @.> wrote: table_annovar.pl ifit_hg38_bin.vcf $HOME/../../mnt/d/BaiduSyncdisk/biodata/humandb/ -buildver hg38 -out ifit_hg38_bin_annovar -remove -protocol refGene,ensGene,1000g2015aug_eas -operation g,g,f -nastring . -xref ~/annovar/example/gene_fullxref.txt -vcfinput My code was shown above. This running code did not prompt any errors or warning. But I just got nothing after running this code. Could you please help me with this issue? Many thanks! screenshot20240827105324.png (view on web) https://github.com/user-attachments/assets/442f3e62-8863-4317-a104-1ef62df72b55 — Reply to this email directly, view it on GitHub <#251>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OCUMRFPQ2ZMYPS4CUTZTPS5RAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DQMJUG4ZDKNY . You are receiving this because you are subscribed to this thread.Message ID: @.>

Oh, sorry, I'm afraid I checked the wrong file. I noticed that the text file has already been annotated, but the vcf file was not.

[kaichop]

VCF should be annotated as well, it is a new VCF file, not the original input.

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On Mon, Aug 26, 2024 at 11:14 PM fanwayne ***@***.***> wrote: Did you check the output file? The output is written to the file ifit_hg38_bin_annovar.hg38_multianno.txt … <#m_-3291927269789100615_> On Mon, Aug 26, 2024 at 10:54 PM fanwayne *@*.*> wrote: table_annovar.pl <http://table_annovar.pl> ifit_hg38_bin.vcf $HOME/../../mnt/d/BaiduSyncdisk/biodata/humandb/ -buildver hg38 -out ifit_hg38_bin_annovar -remove -protocol refGene,ensGene,1000g2015aug_eas -operation g,g,f -nastring . -xref ~/annovar/example/gene_fullxref.txt -vcfinput My code was shown above. This running code did not prompt any errors or warning. But I just got nothing after running this code. Could you please help me with this issue? Many thanks! screenshot20240827105324.png (view on web) https://github.com/user-attachments/assets/442f3e62-8863-4317-a104-1ef62df72b55 <https://github.com/user-attachments/assets/442f3e62-8863-4317-a104-1ef62df72b55> — Reply to this email directly, view it on GitHub <#251 <#251>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OCUMRFPQ2ZMYPS4CUTZTPS5RAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DQMJUG4ZDKNY <https://github.com/notifications/unsubscribe-auth/ABNG3OCUMRFPQ2ZMYPS4CUTZTPS5RAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DQMJUG4ZDKNY> . You are receiving this because you are subscribed to this thread.Message ID: @.*> Oh, sorry, I'm afraid I checked the wrong file. I noticed that the text file has already been annotated, but the vcf file was not. — Reply to this email directly, view it on GitHub <#251 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OGEZP56JXYUAK6YBVDZTPVLFAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJRGQ4DKOBTGA> . You are receiving this because you commented.Message ID: ***@***.***>

[fanwayne]

VCF should be annotated as well, it is a new VCF file, not the original input.
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On Mon, Aug 26, 2024 at 11:14 PM fanwayne @.> wrote: Did you check the output file? The output is written to the file ifit_hg38_bin_annovar.hg38_multianno.txt … <#m_-3291927269789100615_> On Mon, Aug 26, 2024 at 10:54 PM fanwayne @.> wrote: table_annovar.pl http://table_annovar.pl ifit_hg38_bin.vcf $HOME/../../mnt/d/BaiduSyncdisk/biodata/humandb/ -buildver hg38 -out ifit_hg38_bin_annovar -remove -protocol refGene,ensGene,1000g2015aug_eas -operation g,g,f -nastring . -xref ~/annovar/example/gene_fullxref.txt -vcfinput My code was shown above. This running code did not prompt any errors or warning. But I just got nothing after running this code. Could you please help me with this issue? Many thanks! screenshot20240827105324.png (view on web) https://github.com/user-attachments/assets/442f3e62-8863-4317-a104-1ef62df72b55 https://github.com/user-attachments/assets/442f3e62-8863-4317-a104-1ef62df72b55 — Reply to this email directly, view it on GitHub <#251 <#251>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OCUMRFPQ2ZMYPS4CUTZTPS5RAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DQMJUG4ZDKNY https://github.com/notifications/unsubscribe-auth/ABNG3OCUMRFPQ2ZMYPS4CUTZTPS5RAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DQMJUG4ZDKNY . You are receiving this because you are subscribed to this thread.Message ID: @.> Oh, sorry, I'm afraid I checked the wrong file. I noticed that the text file has already been annotated, but the vcf file was not. — Reply to this email directly, view it on GitHub <#251 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OGEZP56JXYUAK6YBVDZTPVLFAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJRGQ4DKOBTGA . You are receiving this because you commented.Message ID: @.**>

Sorry. I rechecked the vcf file. Yes, the vcf file was also annotated. As only 2.1% of input SNPs was annotated with allele frequency by the 1000g2015 database, it looks like the majority were all missing.

[kaichop]

you should use gnomad to annotate allele frequency

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On Mon, Aug 26, 2024 at 11:57 PM fanwayne ***@***.***> wrote: VCF should be annotated as well, it is a new VCF file, not the original input. … <#m_-8093207385278309306_> On Mon, Aug 26, 2024 at 11:14 PM fanwayne *@*.*> wrote: Did you check the output file? The output is written to the file ifit_hg38_bin_annovar.hg38_multianno.txt … <#m_-3291927269789100615_> On Mon, Aug 26, 2024 at 10:54 PM fanwayne @.> wrote: table_annovar.pl <http://table_annovar.pl> http://table_annovar.pl <http://table_annovar.pl> ifit_hg38_bin.vcf $HOME/../../mnt/d/BaiduSyncdisk/biodata/humandb/ -buildver hg38 -out ifit_hg38_bin_annovar -remove -protocol refGene,ensGene,1000g2015aug_eas -operation g,g,f -nastring . -xref ~/annovar/example/gene_fullxref.txt -vcfinput My code was shown above. This running code did not prompt any errors or warning. But I just got nothing after running this code. Could you please help me with this issue? Many thanks! screenshot20240827105324.png (view on web) https://github.com/user-attachments/assets/442f3e62-8863-4317-a104-1ef62df72b55 <https://github.com/user-attachments/assets/442f3e62-8863-4317-a104-1ef62df72b55> https://github.com/user-attachments/assets/442f3e62-8863-4317-a104-1ef62df72b55 <https://github.com/user-attachments/assets/442f3e62-8863-4317-a104-1ef62df72b55> — Reply to this email directly, view it on GitHub <#251 <#251> <#251 <#251>>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OCUMRFPQ2ZMYPS4CUTZTPS5RAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DQMJUG4ZDKNY <https://github.com/notifications/unsubscribe-auth/ABNG3OCUMRFPQ2ZMYPS4CUTZTPS5RAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DQMJUG4ZDKNY> https://github.com/notifications/unsubscribe-auth/ABNG3OCUMRFPQ2ZMYPS4CUTZTPS5RAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DQMJUG4ZDKNY <https://github.com/notifications/unsubscribe-auth/ABNG3OCUMRFPQ2ZMYPS4CUTZTPS5RAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DQMJUG4ZDKNY> . You are receiving this because you are subscribed to this thread.Message ID: @.> Oh, sorry, I'm afraid I checked the wrong file. I noticed that the text file has already been annotated, but the vcf file was not. — Reply to this email directly, view it on GitHub <#251 (comment) <#251 (comment)>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OGEZP56JXYUAK6YBVDZTPVLFAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJRGQ4DKOBTGA <https://github.com/notifications/unsubscribe-auth/ABNG3OGEZP56JXYUAK6YBVDZTPVLFAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJRGQ4DKOBTGA> . You are receiving this because you commented.Message ID: @.***> Sorry. I rechecked the vcf file. Yes, the vcf file was also annotated. As only 2.1% of input SNPs was annotated with allele frequency by the 1000g2015 database, it looks like the majority were all missing. — Reply to this email directly, view it on GitHub <#251 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OAFJBA2Y3Q5CBVEFB3ZTP2MDAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJRGUZDAOBVG4> . You are receiving this because you commented.Message ID: ***@***.***>

[fanwayne]

you should use gnomad to annotate allele frequency
…
On Mon, Aug 26, 2024 at 11:57 PM fanwayne @.> wrote: VCF should be annotated as well, it is a new VCF file, not the original input. … <#m_-8093207385278309306_> On Mon, Aug 26, 2024 at 11:14 PM fanwayne @.> wrote: Did you check the output file? The output is written to the file ifit_hg38_bin_annovar.hg38_multianno.txt … <#m_-3291927269789100615_> On Mon, Aug 26, 2024 at 10:54 PM fanwayne @.> wrote: table_annovar.pl http://table_annovar.pl http://table_annovar.pl http://table_annovar.pl ifit_hg38_bin.vcf $HOME/../../mnt/d/BaiduSyncdisk/biodata/humandb/ -buildver hg38 -out ifit_hg38_bin_annovar -remove -protocol refGene,ensGene,1000g2015aug_eas -operation g,g,f -nastring . -xref ~/annovar/example/gene_fullxref.txt -vcfinput My code was shown above. This running code did not prompt any errors or warning. But I just got nothing after running this code. Could you please help me with this issue? Many thanks! screenshot20240827105324.png (view on web) https://github.com/user-attachments/assets/442f3e62-8863-4317-a104-1ef62df72b55 https://github.com/user-attachments/assets/442f3e62-8863-4317-a104-1ef62df72b55 https://github.com/user-attachments/assets/442f3e62-8863-4317-a104-1ef62df72b55 https://github.com/user-attachments/assets/442f3e62-8863-4317-a104-1ef62df72b55 — Reply to this email directly, view it on GitHub <#251 <#251> <#251 <#251>>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OCUMRFPQ2ZMYPS4CUTZTPS5RAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DQMJUG4ZDKNY https://github.com/notifications/unsubscribe-auth/ABNG3OCUMRFPQ2ZMYPS4CUTZTPS5RAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DQMJUG4ZDKNY https://github.com/notifications/unsubscribe-auth/ABNG3OCUMRFPQ2ZMYPS4CUTZTPS5RAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DQMJUG4ZDKNY https://github.com/notifications/unsubscribe-auth/ABNG3OCUMRFPQ2ZMYPS4CUTZTPS5RAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43ASLTON2WKOZSGQ4DQMJUG4ZDKNY . You are receiving this because you are subscribed to this thread.Message ID: @.> Oh, sorry, I'm afraid I checked the wrong file. I noticed that the text file has already been annotated, but the vcf file was not. — Reply to this email directly, view it on GitHub <#251 (comment) <#251 (comment)>>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OGEZP56JXYUAK6YBVDZTPVLFAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJRGQ4DKOBTGA https://github.com/notifications/unsubscribe-auth/ABNG3OGEZP56JXYUAK6YBVDZTPVLFAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJRGQ4DKOBTGA . You are receiving this because you commented.Message ID: @.> Sorry. I rechecked the vcf file. Yes, the vcf file was also annotated. As only 2.1% of input SNPs was annotated with allele frequency by the 1000g2015 database, it looks like the majority were all missing. — Reply to this email directly, view it on GitHub <#251 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OAFJBA2Y3Q5CBVEFB3ZTP2MDAVCNFSM6AAAAABNFFUUD6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDGMJRGUZDAOBVG4 . You are receiving this because you commented.Message ID: @.**>

Thank you very much. yes gnomad showed more non-missing values.