Beagle removed many sites in the target dataset after imputation

Question

[LCG]

I found no options to control this behavior but if I use Beagle and the target dataset (Simons Genome Diversity Project) is quite different from the reference panel i used (1000 genome), i always have many sites removed, although I have set "impute=false", so what is the cause to this event? and what should I do?

Answer 1

[LCG]

To provide more details, here is the command I ran:

java -Xmx250g -jar $BEAGLE_JAR \ gt=$INPUT_FILE \ ref=${REFERENCE_FILE} \ map=$MAP_FILE \ out=${OUTPUT_FILE%.vcf.gz} \ impute=false \ ne=200000 \ nthreads=64

I found that around six thousands sites removed, most of them are not in the 1000 genomes project.