Generating genetic map file to use as input for shapeit

Question

[sale12302006]

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.

[nataliagru1]

I wish someone could answer this lol

Answer 1

[nataliagru1]

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

Answer 2

[cruzpedro]

Although I haven't used myself, this R package seems to calculate recombination rates/genetic map, if you organism doesn't have a canonical map: https://rdrr.io/github/PhHermann/LDJump/f/README.md