Beagle phasing without map and reference parameters

Question

[Shicheng Guo]

Hi All,

I just find beagle can do the phasing without map and reference parameters. Anyone can tell me how it works? What's the difference between phasing with map and reference parameters?

1) phasing without parameters

java -Djava.io.tmpdir=./temp/ -Xmx32g -jar beagle.16May19.351.jar impute=false gt=Exome.vcf out=Exome.vcf.phasing

2) phasing with map and reference parameters

java -Djava.io.tmpdir=./temp/ -Xmx32g -jar beagle.16May19.351.jar gt=Exome.vcf ref=chr22.1kg.phase3.v5a.EUR.vcf.gz map=plink.chr22.GRCh37.map out=Exome_phasing_VCF