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szpiech / selscan

Haplotype based scans for selection
GNU General Public License v3.0
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EHH output interpretation #72

Closed sadiexiaoyu closed 2 years ago

sadiexiaoyu commented 2 years ago

Hi, Szpiech, thank you for the cool software. I am running EHH to get the EHH decay plot, and I have several questions about the output files. First of all, how can I use the output file .colormap draw the EHH decay plot? Secondly, what does the output file .out mean? For example, -99968 -99968.000000 0.122342 0.015415 0.016067 -99802 -99802.000000 0.122342 0.015415 0.016067 -99801 -99801.000000 0.122342 0.015415 0.016067 -99775 -99775.000000 0.122342 0.015415 0.016067 -99734 -99734.000000 0.122342 0.015415 0.016067 -99649 -99649.000000 0.122342 0.015415 0.016067 -99617 -99617.000000 0.122342 0.015415 0.016067 -99475 -99475.000000 0.122342 0.015415 0.016067 -99312 -99312.000000 0.122342 0.015415 0.016067 -99190 -99190.000000 0.122342 0.015415 0.016067 -99142 -99142.000000 0.122342 0.015415 0.016067 -99065 -99065.000000 0.122342 0.015415 0.016067 -98972 -98972.000000 0.122342 0.015415 0.016067 -98746 -98746.000000 0.122342 0.015415 0.016067 -98557 -98557.000000 0.122342 0.015415 0.016067 -98472 -98472.000000 0.122342 0.015415 0.016067 -98350 -98350.000000 0.122342 0.015415 0.016067 -97959 -97959.000000 0.122342 0.015415 0.016067 -97735 -97735.000000 0.122342 0.015415 0.016067 -97444 -97444.000000 0.122342 0.015415 0.016067 -97184 -97184.000000 0.122342 0.015415 0.016067 -97096 -97096.000000 0.122342 0.015415 0.016067 -97038 -97038.000000 0.122342 0.015415 0.016067

In the selscan manual, it says that the output file of EHH include physicalPos, geneticPos, 1 EHH, 0EHH. But it seems not the case...did I miss anything? Looking forward to your reply! Thanks!

szpiech commented 2 years ago

Hi there,

The file you've quoted here is the file you can use to generate the decay curves. The manual is a little out of date, sorry about that. The columns refer to

physicalPos relative to core SNP, geneticPos relative to core SNP, 1 EHH, 0EHH, total EHH (all 0 and 1 haplotypes together)

So you get negative values for the positions when the location is upstream of the core snp, and positive values when the position is downstream of the core.

Hope this helps,

Zach

sadiexiaoyu commented 2 years ago

Thank you very much for the quick reply!