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I recently used Beagle 4.1 to get phase information for whole genomes for several individuals. The command I used was:
java -Xmx170g -jar $BEAGLE gt=<vcf_file> impute=false out=<output_name>
Upon looking at the output, I was surprised to find that ALL sites in ALL individuals had been phased for each chromosome that I inspected. I know Beagle is supposed to work quite well, but this seems a bit strange. I was expecting to find a mixture of phased blocks interspaced by unphased sites. Also, it seems to have imputed genotypes even though I specified 'impute=false'.
Is this output typical of what others have seen? If not, is there something obvious I'm doing wrong?
I'm a newbie to phasing so apologies for the naivete.
java -Xmx170g -jar $BEAGLE gt=<vcf_file> impute=false out=<output_name>
Upon looking at the output, I was surprised to find that ALL sites in ALL individuals had been phased for each chromosome that I inspected. I know Beagle is supposed to work quite well, but this seems a bit strange. I was expecting to find a mixture of phased blocks interspaced by unphased sites. Also, it seems to have imputed genotypes even though I specified 'impute=false'.
Is this output typical of what others have seen? If not, is there something obvious I'm doing wrong?
I'm a newbie to phasing so apologies for the naivete.