output flie contained nothing

[Morriyaty]

Hi!

When I used hapbin to calculate XPEHH, I found my result file contained nothing. My map file was obtained with PLINK (plink --vcf LG01.vcf.gz --allow-extra-chr --recode --out test). The map file was like this: LG01 . 0 400057 LG01 . 0 400063 LG01 . 0 400066 LG01 . 0 400102 But I found the test map data was like this: 22 38 0 16051250 22 39 0 16051269 22 40 0.0123386217370137 16051432 22 41 0.0123386217370137 16051453 22 42 0.0123386217370137 16051453

Did my map file have some error or some unexpected probably error?

[Morriyaty]

By the way, I have been told by hapbin that : Haplotypes in population A: 10 Haplotypes in population B: 14 Threads: 32 393000/393901/393901393901 Calculations took 1485.98ms

valid loci: 0: 0

[prenderj]

Hi

Looks like there may be a couple of issues with your file. The second column is meant to be a variant id, so cant all be "." and looks like your genetic distance (3rd) column may all be 0. XP-EHH requires the genetic distance.

Cheers James

On Sat, 5 Jun 2021 at 11:00, wyj-lzu @.***> wrote:

Hi!

When I used hapbin to calculate XPEHH, I found my result file contained nothing. My map file was obtained with PLINK (plink --vcf LG01.vcf.gz --allow-extra-chr --recode --out test). The map file was like this: LG01 . 0 400057 LG01 . 0 400063 LG01 . 0 400066 LG01 . 0 400102 But I found the test map data was like this: 22 38 0 16051250 22 39 0 16051269 22 40 0.0123386217370137 16051432 22 41 0.0123386217370137 16051453 22 42 0.0123386217370137 16051453

Did my map file have some error or some unexpected probably error?

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/evotools/hapbin/issues/65, or unsubscribe https://github.com/notifications/unsubscribe-auth/AB5OYGQLQLAQHKTVVYWH3ZTTRHYSPANCNFSM46ELFDXA .

[Morriyaty]

OK，I got it. Thanks!