williamslab / ibis

Algorithm for rapid, phase-free detection of long identical by descent segments
GNU General Public License v3.0
17 stars 7 forks source link

Error using command to add the genetic map file to the bim file #4

Closed lakishadavid closed 2 years ago

lakishadavid commented 2 years ago

I'm running into an error using ./add-map-plink.pl to add the genetic map to the bim file.

I tried to use the IBIS ./add-map-plink.pl on an autosome map file created from plink map files hosted on Brian Browning's beagle website. I get the following error message for each line in the map file. (I couldn't use the maps in your documentation because the links you provide don't go anywhere.)

Argument "." isn't numeric in numeric lt (<) at ./add-map-plink.pl line 85, <MAP> line 65706.

Here are the first three lines of the autosome genetic map file. Chromosomes 1 - 22 are in the same file.

1 . 0 55550
1 . 0.080572 82571
1 . 0.092229 88169

Here is the command that I use to add the genetic map file.

./add-map-plink.pl plink.bim plink_GRCh38_map/plink.autosome.GRCh38.map > plink_gm.bim

Any advice on what I should do to fix this error?

Note: The ./ibis command does run in that it gives me an output of Total Genetic Length in use:2999.915039 and Total Segments Found: 2474.

lakishadavid commented 2 years ago

I used the link in the email from Amy Williams. I have the program working fine now. Thank you. This issue can be closed.

Link to map file https://ftp.ncbi.nlm.nih.gov/hapmap/recombination/2011-01_phaseII_B37/