Why don't my map files contain cM values?

Question

[alistairhudson94]

Hi there - I'm new to plink and genomics more generally. I am trying to generate a .map file with cM values using phased VCFs in PLINK (v1.90b6.21), but am having no luck getting the cM values despite using phased data. I need cM values for use with hap-ibd.

My vcfs were phased first with beagle and then shapeit, and look like this:

#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  AI1     AI12    AI13    AI14    AI15    AI16    AI17    AI18    AI19    AI2     AI20    AI21    AI22    AI3     AI4     AI5     AI6     AI7     AI8     AI9
chr10   5246    .       T       A       .       PASS    .       GT      0|0     0|0     0|1     0|0     0|0     0|1     0|0     0|0     0|0     0|0     0|0     0|1     0|1     0|0     0|0     0|0     0|1     0|1     0|1     0|1
chr10   5250    .       G       A       .       PASS    .       GT      0|0     0|0     0|1     0|0     0|0     0|1     0|0     0|0     0|0     0|0     0|0     0|1     0|1     0|0     0|0     0|0     0|1     0|1     0|1     0|1
chr10   7339    .       A       G       .       PASS    .       GT      0|0     0|0     0|0     1|1     1|1     1|1     1|1     1|1     1|1     1|1     1|1     1|1     1|1     1|1     1|1     1|1     1|1     0|0     1|1     1|1
chr10   9662    .       C       T       .       PASS    .       GT      0|0     0|0     0|0     0|0     0|0     0|1     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0
chr10   12614   .       G       A       .       PASS    .       GT      0|0     0|0     0|0     0|0     0|0     1|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0     0|0

To generate the map files, I've tried a dozen variations of:

for POP in X Y Z
do
    plink --vcf $VCFDIR/SNPs_phased_chromosomes_dataset1_${POP}.recode.vcf --map --out ${POP}

    plink --bfile ${POP} --recode rlist tab --set-missing-var-ids @:# --out ${POP}.map 
done

All my .map files have 0 for every value of the cM column.

Am I doing something wrong? I have .bed files for these populations, but I don't know how to check that phase information is included in them, nor do I know why it wouldn't be there considering that the files are phased.

Thanks for any help anyone can offer.

Answer 1

[rimgubaev]

If you want cM data it usually means, that you have a genetic map constructed for the experimental cross which allows calculating the genetic distance between the markers in cM (centimorgans). Alternatively, it is possible to convert physical distance (megabases, Mb) to genetic distances (centimorgans, cM), where 1 Mb equals to 1 cM, so you could divide your physical distance (POS column) by 1000000. However, this would be a very rough estimate.

By the way what type of organism are you working with (plant or animal)? Is it an experimental cross (F2, BC) or a genetic diversity panel?

Ideally, if you have the experimental cross data with a large number of progeny you should first consider building a genetic map to obtain true cM values for example in R/QTL.

[alistairhudson94]

Reformatting my existing ref maps and combining them all into one file worked. Thanks!

[alistairhudson94]

Thanks for responding! This was really helpful as I now think I have the data I need to go off of.

My data is from multiple wild populations of P. reticulata (guppies, a small fish).

I do have recombination maps for guppies in general, but because it looked different from what I'd expected and I found others asking about generating the maps online, I thought I should be able to do it from what I had.

The recombination maps I have access to have a slightly different format, and are smoothed and given per-chromosome for guppies as a whole.

pos         Genetic_Map             COMBINED_rate
111592      2.02646782904847        0.209091655087261
231473      2.05153394575198        0.214261119445609
357843      2.07861012341633        0.223968758855395
441137      2.09726537721643        0.236499564551847

vs the format of a map generated by PLINK

10      chr10:5246      0       5246
10      chr10:5250      0       5250
10      chr10:7339      0       7339
10      chr10:9662      0       9662

If I can reformat what I might be able to get this to work...