Alleles must be coded 0/1 only

[huangl07]

hello xpehh users，how to understanc alleles must be coded 0/1 only?

does it means no missing in ref vcfs?

[Chen-SHuangHui]

I have this question, too. But I guess it means that the data must be biallelic.

[szpiech]

Yep, that’s correct.

-Zachary

Le ven. 17 juin 2022 à 11:34 AM, Chen Shuanghui @.***> a écrit :

I have this question, too. But I guess it means that the data must be biallelic.

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[huangl07]

while I have already check my file , it is biallelic varaint

you may check the file ,thankyou sca10010-1.vcf.gz sca10010-2.vcf.gz

[huangl07]

how ever when I filtered all missing variant, the error is gone!

I think there could be fixed ?

but why the calculated can not do with the missing allele?

[szpiech]

Hello,

Selscan does not currently support missing data entries. So you will need to either filter/impute your loci with missing data in order to run the program.

Zachary

Le dim. 19 juin 2022 à 9:40 PM, huangl07 @.***> a écrit :

how ever when I filtered all missing variant, the error is gone!

I think there could be fixed ?

but why the calculated can not do with the missing allele?

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[huangl07]

Thank you for your replay!

[szpiech]

Hello,

This is correct that missing data is not currently supported.

-Zachary

Le ven. 17 juin 2022 à 3:19 AM, huangl07 @.***> a écrit :

hello xpehh users，how to understanc alleles must be coded 0/1 only?

does it means no missing in ref vcfs?

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[original10012]

Can you share the filtered code?

This error still exists

[original10012]

ERROR: Haplotypes from test1.vcf.gz and test2.vcf.gz do not have the same number of loci. Does that mean we need to keep the same number of loci

[szpiech]

Hello,

Yes this is correct, the two vcf (or other format) files you pass should have the same loci in each file.

-Zachary

Le jeu. 15 déc. 2022 à 9:23 AM, original10012 @.***> a écrit :

ERROR: Haplotypes from test1.vcf.gz and test2.vcf.gz do not have the same number of loci. Does that mean we need to keep the same number of loci

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[original10012]

Hello, Yes this is correct, the two vcf (or other format) files you pass should have the same loci in each file. … -Zachary Le jeu. 15 déc. 2022 à 9:23 AM, original10012 @.> a écrit : ERROR: Haplotypes from test1.vcf.gz and test2.vcf.gz do not have the same number of loci. Does that mean we need to keep the same number of loci — Reply to this email directly, view it on GitHub <#85 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABAKRQXT6EG3PILR23E4MBDWNMSUXANCNFSM5ZBKQ7GA . You are receiving this because you commented.Message ID: @.>

Thank you for your reply. I have successfully solved this problem.