beagle map

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Sep 15, 2021, 1:55:19 PM9/15/21

to TASSEL - Trait Analysis by Association, Evolution and Linkage

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I pre-processed my genotype file with Tassel > Impute> Remove indels for input for Beagle.

Then I tried below.

Command line: java -Xmx16360m -jar beagle.28Jun21.220.jar

nthreads=2

gt=beagled_chr10.vcf.gz

excludemarkers=chr10_excluded_markers.txt

out=beagle_modified_chr10.vcf

No genetic map is specified: using 1 cM = 1 Mb

ERROR: invalid ALT allele at 10:2331141 [+]

##############################################

chr10_excluded_markers.txt

looks like this:

10:2331141

Where can I find genetic map file for the maize preferably separate for each chromosome?

I appreciate any help.

Caesarius

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