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