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Atkinson-Lab / Tractor

Scripts for implementing the Tractor pipeline
MIT License
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Differences in AF between original version and v 1.1.0 #27

Closed nick338 closed 6 months ago

nick338 commented 8 months ago

Hello,

I ran tractor on the same cohort using the same rfmix output and noticed that the AF for some variants differed between my original tractor output and the v1.1.0 output. Was there any difference in how AF was calculated in the new version of tractor? Thanks for any help you can provide.

JasonTan-code commented 8 months ago

Hi, do you mean the AF is different for some variants or for all variants? If possible, can you send me a few variants through my email (Taotao.Tan@bcm.edu)? You may subset a few variants in the file of anc.hapcount.txt and anc.dosage.txt and share them with me.

nirav572 commented 6 months ago

Hi @nick338,

Thanks for pointing this out. There was a small error in dosage computation in the extract_tracts.py script that is now fixed. Please try again with the updated script.

Thank you.