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2 hours ago by


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?

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