Hello Biostars community,
I'm currently conducting haplotype-based association studies using phased haplotypes generated with SHAPEIT. While I have successfully phased my haplotypes, I'm encountering challenges in integrating them into genetic analysis software like GCTA.
Could anyone share their experiences with haplotype-based association studies? Specifically:
Which software tools have you found effective for analyzing haplotype data in genome-wide association studies? How did you convert or use phased haplotypes (such as those from SHAPEIT) in these software tools? Are there resources or references you found helpful in this process?
I have explored suggestions involving PLINK, but recommendations against using --hap have been noted. Any insights or recommendations based on your experiences would be greatly appreciated! Thank you!
