Error count of the derived haplotypes

[liuqi-C]

When I use --ehh to calculate the EHH curves for the ancestral and derived haplotypes, I think the result is wrong.
e.g. for chrxxx:G:A, In my vcf, allele count for A (derived) is 15 and for G (ancestral) is 47. But when I get the result files with suffix "der.colormap" and "anc.colormap", the line number for these files is 4 and 58.

In addition, I use the "cal_ehh" function in rehh package in R, I get different EHH curve for the same SNP and input data.

Could you help me to solve this problem?

[szpiech]

Hi, We're currently making some major changes to the code base, so we can look more carefully at this. Zachary

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On Tue, Jun 25, 2024 at 9:20 AM liuqi ***@***.***> wrote: When I use --ehh to calculate the EHH curves for calculate EHH curves for the ancestral and derived haploytpes, I think the result is wrong. e.g. for chr16:76647336:G:A, In my vcf, allele count for A (derived) is 15 and for G (ancestral) is 47. But when I get the result files with suffix "der.colormap" and "anc.colormap", the line number for these files is 4 and 58. Could you help me to solve this problem? — Reply to this email directly, view it on GitHub <#117>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABAKRQX32V4PMYO2CFY6ECTZJFVBXAVCNFSM6AAAAABJ327TUWVHI2DSMVQWIX3LMV43ASLTON2WKOZSGM3TENRYHAZTAOI> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>