Error: More than 100 obvious strand flips have been detected. Please check strand. Imputation cannot be started!
Statistics: Alternative allele frequency > 0.5 sites: 0 Reference Overlap: 99.80% Match: 426,485 Allele switch: 66,772 Strand flip: 23,263 Strand flip and allele switch: 13,805 A/T, C/G genotypes: 642 Filtered sites: Filter flag set: 0 Invalid alleles: 0 Duplicated sites: 286 NonSNP sites: 0 Monomorphic sites: 0 Allele mismatch: 465 SNPs call rate < 90%: 0
beagle provided a java tool called conform-gt https://faculty.washington.edu/browning/conform-gt.html
a program for making alleles in a VCF file to be consistent with a reference VCF file, see an example:
java -jar conform-gt.24May16.cee.jar gt=input.vcf.gz chrom=$i ref=chr22.1kg.phase3.v5a.EUR.vcf.gz out=output.chr22.beagle.vcf.gz













