I did a variant calling of 200 genotypes with freebayes. I filtered for the DP and GQ values and the genotypes that did not pass the filter were set to
./.. I now want to impute these filtered vcf files with BEAGLE v5.1. But it is giving me the following error:
java.lang.IllegalArgumentException: java.lang.IllegalArgumentException: ERROR: inconsistent number of alleles for sample Sample_1469 at marker [chr4A 305381905 . G A]
What could be the problem? I had a look at the position and it looks like this:
This is missing data. Could it be the reason? If yes, how could I deal with this?