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.OUT file blank #88
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Hi there,
The default behavior of selscan is to skip calculations that are close to
large gaps between loci or are close to chromosome end points. If your data
is very sparse, you could change the maximum gap size with the --max-gap
flag. If you are analyzing very small regions (e.g., perhaps you have
simulated a 100kb region), you might want to use the --trunc-ok flag, which
allows the program to compute the integration even if the EHH curve hasn't
reached the default 0.05. I would caution against using --trunc-ok in very
sparse data, as it could create weird biases. It is really best used for
analyzing short regions of simulated data.
There is a small program for interpolating genetic map disances on my
github (https://github.com/szpiech/predictGMAP) that does linear
interpolation to get a genetic map file for all your sites (this also has a
--max-gap flag, which you could choose to set very high if you are losing
too many sites while processing). Eventually, I should add this
functionality directly into selscan, but you can try this program if you
are having trouble.
Let me know if you have any troubles.
Zachary
…On Wed, Sep 21, 2022 at 2:54 PM aramesh97 ***@***.***> wrote:
Hello,
I have successfully got the selscan to work with the --pmap flag and by
providing a physical map of my chromosome. I have also used impute on my
vcf to phase the file but my .out file is empty. In the log I get two types
of errors:
1. WARNING: Reached chromosome edge before EHH decayed below 0.05.
Skipping calculation at position 13288828 id: chr21:13288828:G:A
2. WARNING: Reached a gap of 229066bp > 200000bp. Skipping calculation
at position 13850378 id: chr21:13850378:G:C
Can you please help me with this? Any explanation on what I can do to
avoid this is much appreciated
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Hello,
I have successfully got the selscan to work with the --pmap flag and by providing a physical map of my chromosome. I have also used impute on my vcf to phase the file but my .out file is empty. In the log I get two types of errors:
Can you please help me with this? Any explanation on what I can do to avoid this is much appreciated
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