Question: Generating genetic map file to use as input for shapeit
3
gravatar for sale12302006
3.5 years ago by
sale1230200630
United Kingdom
sale1230200630 wrote:

Dear All,

Can someone help me with this, please? I am trying to produce genetic map file that will contain the following three columns below from vcf file:

pposition    rrate     gposition
72765        0.12455   0.00000
94172        0.12458   0.00266
94426        0.12461   0.00269
95949        0.12461   0.00288
98087        0.12460   0.00315

Where:

  • First column: The physical position (bp)
  • Second column: The recombination rate (cM/Mb)
  • Third column: The genetic position (cM)

Your help would be appreciated.

genome • 1.6k views
ADD COMMENTlink modified 4 weeks ago by nataliagru120 • written 3.5 years ago by sale1230200630

I wish someone could answer this lol

ADD REPLYlink written 7 weeks ago by nataliagru120

It is actually rather challenging to produce a genetic map file from scratch. ShapeIT does have the option to exclude the genetic map and use a function --roh or "recombination rate". This is simply one value. You should be able to find a recombination rate value in scientific literature for the species you are studying. If you are using hapmap data or 1000 genome data they have genetic maps provided, links to these genetic maps are in the ShapeIT manual . See manual here for more detail: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#gettingstarted

ADD REPLYlink written 5 weeks ago by nataliagru120
0
gravatar for nataliagru1
4 weeks ago by
nataliagru120
nataliagru120 wrote:

It is actually rather challenging to produce a genetic map file from scratch. ShapeIT does have the option to exclude the genetic map and use a function --roh or "recombination rate". This is simply one value. You should be able to find a recombination rate value in scientific literature for the species you are studying. If you are using hapmap data or 1000 genome data they have genetic maps provided, links to these genetic maps are in the ShapeIT manual . See manual here for more detail: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html#gettingstarted

ADD COMMENTlink written 4 weeks ago by nataliagru120
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